{"id":196,"date":"2016-12-23T23:36:07","date_gmt":"2016-12-23T23:36:07","guid":{"rendered":"https:\/\/sites.bioe.uw.edu\/dratner\/?page_id=196"},"modified":"2025-09-17T08:18:17","modified_gmt":"2025-09-17T15:18:17","slug":"publications","status":"publish","type":"page","link":"https:\/\/sites.bioe.uw.edu\/daggett\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<ul>\n<li>Nick, S.E., Bryers, J.D., <strong>Daggett, V.<\/strong> Layer-by-layer functionalized gauze with designed alpha-sheet peptides inhibits <em> coli<\/em> and <em>S. aureus<\/em> biofilm formation. <em>J. Biomed. Mater. Res. A<\/em>, 113: e37879, 2025. \u00a0<a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jbm.a.37879\">https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jbm.a.37879<\/a><\/li>\n<li>Prosswimmer, T., Nick, S.E., Bryers, J.D., <strong>Daggett, V<\/strong>. Designed de novo a-sheet Peptides Destabilize Bacterial Biofilms and Increase the Susceptibility of <em> coli <\/em>and <em>S. aureus <\/em>to Antibiotics, <em>International Journal of Molecular Sciences<\/em>, 25: 7024, 2025.<br \/>\n<a href=\"https:\/\/www.mdpi.com\/1422-0067\/25\/13\/7024\">https:\/\/www.mdpi.com\/1422-0067\/25\/13\/7024<\/a><\/li>\n<li>Chen, A., Shea, D., <strong>Daggett, V.<\/strong> Performance of SOBA-AD blood test in discriminating Alzheimer\u2019s disease patients from cognitively unimpaired controls in two independent cohorts. <em>Nature Scientific Reports<\/em>, 14: 7946, 2024.<br \/>\n<a href=\"https:\/\/www.nature.com\/articles\/s41598-024-57107-w\">https:\/\/www.nature.com\/articles\/s41598-024-57107-w<\/a><\/li>\n<li>Prosswimmer, T., Heng, A., <strong>Daggett, V<\/strong>. Mechanistic insights into the role of amyloid-b in innate immunity. <em>Nature Scientific Reports<\/em>, 14: 5376, 2024. <a href=\"https:\/\/www.nature.com\/articles\/s41598-024-55423-9\">https:\/\/www.nature.com\/articles\/s41598-024-55423-9<\/a><\/li>\n<li>Hsu, C.-C., Templin, A.T., Prosswimmer, T., Shea, D., Li, J., Brooks-Worrell, B., Kahn, S.E., <strong>Daggett, V<\/strong>. Human islet amyloid polypeptide-induced \u03b2-cell cytotoxicity is linked to formation of a-sheet structure. <em>Protein Science<\/em>, 33, e4854, 2024. <a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/pro.4854\">https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/pro.4854<\/a><\/li>\n<li>Bleem, A. Prosswimmer, T., Chen, R., Hady, T., Li, J., Bryers, J.D., <strong>Daggett, V<\/strong>. Designed \u03b1-sheet peptides disrupt uropathogenic\u00a0<em> coli<\/em>\u00a0biofilms rendering bacteria susceptible to antibiotics and immune cells, <em>Nature Scientific Reports<\/em>, 13, 9297, 2023. <a href=\"https:\/\/www.nature.com\/articles\/s41598-023-36343-6\">https:\/\/www.nature.com\/articles\/s41598-023-36343-6<\/a><\/li>\n<li>Shea, D., Colasurdo, E., Smith, Al., Paschall, C., Jayadev, S., Keene, C.D., Galasko, D., Do, A., Li, G., Peskind, E., Daggett, V., SOBA: Development and Testing of a Soluble Oligomer Binding Assay for Detection of Amyloidogenic Toxic Oligomers, Proc. Natl. Acad. Sci. USA, 119(50), e2213157119, 2022.<\/li>\n<li>Prosswimmer, T., <strong>Daggett, V.<\/strong> The role of a-sheet structure in amyloidogenesis: characterization and implications. Royal Society, <em>Open Biology<\/em>, <em>2<\/em>: 91-110, 2022.<\/li>\n<li>Shea, D., <strong>Daggett, V.<\/strong> Amyloid-\u03b2 Oligomers: Multiple Moving Targets, <em>Biophysica<\/em>, <em>2<\/em>: 91-110, 2022. <a href=\"https:\/\/doi.org\/10.1098\/rsob.220261\">https:\/\/doi.org\/10.1098\/rsob.220261<\/a><\/li>\n<li>Childers, M.C., Geeves, M., Daggett, V., Regnier, M. Modulation of post-powerstroke dynamics in myosin II by 2\u2032-deoxy-ADP.\u00a0<strong>Arch Biochem Biophys<\/strong>, 699:108733, 2020. [<a href=\"https:\/\/doi.org\/10.1016\/j.abb.2020.108733\">DOI<\/a>]<\/li>\n<li>Demakis, C., Childers, M.C., Daggett,\u00a0 V. Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues.\u00a0<strong>Protein Sci<\/strong>, 30(2):391-407, 2020. [<a href=\"https:\/\/doi.org\/10.1002\/pro.3998\">DOI<\/a>]<\/li>\n<li>Childers, M.C., Daggett, V. Edge strand dissociation and conformational changes in transthyretin under amyloidogenic conditions. <strong>Biophys J<\/strong>, 119(10):1995-2009, 2020. [<a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2020.08.043\">DOI<\/a>]<\/li>\n<li>Ma, W., Childers, M.C., Murray, J., Moussavi-Harami, F., Gong, H., Weiss, R.S., Daggett, V., Irving, T.C., Regnier, M. Myosin dynamics during relaxation in mouse soleus muscle and modulation by 2\u2032-deoxy-ATP. <strong>J<\/strong><strong>\u00a0Physiol<\/strong>, 598(22):5165-5182, 2020. [<a href=\"https:\/\/doi.org\/10.1113\/jp280402\">DOI<\/a>]<\/li>\n<li>Bromley, D., Daggett, V. Tumorigenic p53 mutants undergo common structural disruptions including conversion to \u03b1-sheet structure.\u00a0<b>Protein Sci<\/b>, 29(9):1983-1999,\u00a02020. [<a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/pro.3921\">DOI<\/a>]<\/li>\n<li>Toofanny, R.D., Calhoun, S., Jonsson, A.L., Daggett, V. Shared unfolding pathways of unrelated immunoglobulin-like beta-sandwich proteins.\u00a0<b>Protein Eng Des Sel<\/b>, 32(7):331-345, 2019. [<a href=\"https:\/\/doi.org\/10.1093\/protein\/gzz040\">DOI<\/a>]<\/li>\n<li>Childers, M.C., Daggett, V., Drivers of \u03b1-sheet formation in transthyretin under amyloidogenic conditions,\u00a0<b>Biochemistry<\/b>,\u00a058(44):4408-4423, 2019. [<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.biochem.9b00769\">DOI<\/a>]<\/li>\n<li>Powers, J.D., Yuan, C.C., McCabe, K.J., Murray, J.D., Childers, M.C., Flint, G.V., Moussavi-Harami, F., Mohran, S., Castillo, R., Zuzek, C., Ma, W., Daggett, V., McCulloch, A.D., Irving, T.C., Regnier, M. Cardiac myosin activation with 2-deoxy-ATP via increased electrostatic interactions with actin.\u00a0<b>Proc Natl Acad Sci USA<\/b>,\u00a0116(23):11502-11507, 2019. [<a href=\"https:\/\/doi.org\/10.1073\/pnas.1905028116\">DOI<\/a>]<\/li>\n<li>Shea, D., Hsu, C.-C., Bi, T., Paranjapye, N., Childers, M., Cochran, J., Tomberlin, C.P., Wang, L., Paris, D., Zonderman, J., Varani, G., Link, C., Mullan, M., Daggett, V., \u03b1-sheet secondary structure in amyloid \u03b2-peptide drives aggregation and toxicity in Alzheimer\u2019s disease.\u00a0<b>Proc Natl Acad Sci USA<\/b>,\u00a0116(18):8895-8900, 2019. [<a href=\"https:\/\/doi.org\/10.1073\/pnas.1820585116\">DOI<\/a>]<\/li>\n<li>Ferina, J., Daggett, V. Visualizing protein folding and unfolding.\u00a0<b>J Mol Biol<\/b>,\u00a0431(8):1540-1564, 2019. [<a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2019.02.026\">DOI<\/a>]<\/li>\n<li>Bi, T.M., Daggett, V. The role of alpha-sheet in amyloid oligomer aggregation and toxicity,\u00a0<b>Yale J Biol Med<\/b>,\u00a091(3):247-255, 2018. [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6153628\/pdf\/yjbm_91_3_247.pdf\">PDF<\/a>]<\/li>\n<li>Gianni, S., McCully, M.E., Malagrino, F., Bonetti, D., De Simone, A., Brunori, M., Daggett, V. A carboxylate to amide substitution tunes fold switching in a protein domain.\u00a0<b>Angew Chem<\/b>,\u00a057(39):12795-12798, 2018. [<a href=\"https:\/\/doi.org\/10.1002\/anie.201807723\">DOI<\/a>]<\/li>\n<li>Paranjapye, N., Daggett, V. De novo designed alpha-sheet peptides inhibit functional amyloid formation of Streptococcus mutans biofilms,\u00a0<b>J Mol Biol<\/b>,\u00a0430(20)<i>:<\/i>3764-3773, 2018. [<a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2018.07.005\">DOI<\/a>]<\/li>\n<li>Childers, M.C., Towse, C.-L., Daggett, V. Molecular dynamics-derived libraries for D-amino acids within homochiral and heterochiral polypeptides.\u00a0<b>Protein Eng Des Sel<\/b>,\u00a031(6)<i>:<\/i>191-204, 2018. [<a href=\"https:\/\/academic.oup.com\/peds\/advance-article-abstract\/doi\/10.1093\/protein\/gzy016\/5051148\">DOI<\/a>]<\/li>\n<li>Bleem, A., Christiansen, G., Madsen, D.J., Maric, H., Str\u00f8mgaard K., Bryers, J.D., Daggett, V., Meyer, R.L., Otzen, D.E. Protein engineering reveals mechanisms of functional amyloid formation in Pseudomonas aeruginosa biofilms.\u00a0<b>J Mol Biol<\/b>, 430(20):3751-3763, 2018. [<a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2018.06.043\">DOI<\/a>]<\/li>\n<li>Childers, M.C., Daggett, V. Validating molecular dynamics simulations against experimental observables in light of underlying conformational ensembles.\u00a0<b>J Phys Chem B<\/b>,\u00a0122(26):6673-6689, 2018. [<a href=\"http:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jpcb.8b02144\">DOI<\/a>]<\/li>\n<li>Maris, N.L, Shea, D., Bleem, A., Bryers, J.D., Daggett, V. Chemical and physical variability in structural isomers of an L\/D alpha-sheet peptide designed to inhibit amyloidogenesis.\u00a0<b>Biochemistry<\/b>,\u00a057(5):507-510, 2018. [<a href=\"http:\/\/pubs.acs.org\/doi\/10.1021\/acs.biochem.7b00345\">DOI<\/a>]<\/li>\n<li>Bleem, A. , Francisco, R., Bryers, J.D., Daggett, V. Designed alpha-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilm.\u00a0<b>NPJ Biofilms Microbiomes<\/b>,\u00a0<i>3<\/i>:16, 2017. [<a href=\"http:\/\/dx.doi.org\/10.1038\/s41522-017-0025-2\">DOI<\/a>]<\/li>\n<li>Cheng, C.C., Kolds\u00f8, H., Van der Kamp, M.W., Schi\u00f8tt, B., Daggett, V., Simulations of Membrane-bound Diglycosylated Human Prion Protein Reveal Potential Protective Mechanisms against Misfolding.<b>\u00a0J Neurochem<\/b>,\u00a0142(1):171-182, 2017. [<a href=\"http:\/\/dx.doi.org\/10.1111\/jnc.14044\">DOI<\/a>]<\/li>\n<li>Towse, C.-L., Akke, M., Daggett, V. The Dynameomics Entropy Dictionary: A large-scale assessment of conformational entropy across protein fold space.<b>\u00a0J Phys Chem B<\/b>,\u00a0121(16):3933-3945, 2017. [<a href=\"http:\/\/dx.doi.org\/10.1021\/acs.jpcb.7b00577\">DOI<\/a>]<\/li>\n<li>Childers, M.C., Daggett, V. Insights from molecular dynamics simulations for computational protein design.\u00a0<b>Mol Syst Des Eng<\/b>, 2(1):9-33, 2017. [<a href=\"http:\/\/dx.doi.org\/10.1039\/C6ME00083E\">DOI<\/a>]<\/li>\n<li>Nowakowski, S.G., Regnier, M., Daggett, V. Molecular mechanisms underlying deoxy-ADP.Pi activation of pre-powerstroke myosin.\u00a0<b>Protein Sci<\/b>,\u00a026(4): 749-762, 2017. [<a href=\"http:\/\/dx.doi.org\/10.1002\/pro.3121\">DOI<\/a>]<\/li>\n<li>Bromley, D., Bauer, M.R., Fersht, A.R., Daggett, V. An\u00a0<em>in silico\u00a0<\/em>algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein.\u00a0<strong>Protein Eng Des Sel<\/strong>, 29(9):377-390, 2017. [<a href=\"https:\/\/doi.org\/10.1093\/protein\/gzw035\">DOI<\/a>]<\/li>\n<li>Bleem, A., Daggett, V. Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering.\u00a0<b>Biotechnology and Bioengineering\u00a0<\/b><i>114\u00a0<\/i>: 7-20, 2017. [<a href=\"http:\/\/dx.doi.org\/10.1002\/bit.26059\">DOI<\/a>]<\/li>\n<li>Childers, M.C., Towse, C.-L., Daggett, V. The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: Tools for protein design.\u00a0<b>Protein Eng Des Sel<\/b>, 29(7):271-280, 2016. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzw023\">DOI<\/a>]<\/li>\n<li>Kellock, J., Hopping, G., Caughey, B., Daggett, V. Peptides composed of alternating L- and D-amino acids inhibit amyloidogenesis in three distinct amyloid systems independent of sequence.\u00a0<b>J Mol Biol<\/b>, 428(11):2317-2328, 2016. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2016.03.013\">DOI<\/a>]<\/li>\n<li>Towse, C.-L., Vymetal, J., Vondrasek, J., Daggett, V. Insights into unfolded proteins from the intrinsic \u03c6\/\u03c8 propensities of the AAXAA host-guest series.\u00a0<b>Biophys J<\/b>, 110(2):348-361, 2016. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2015.12.008\">DOI<\/a>]<\/li>\n<li>Towse, C.-L., Rysavy, S.J., Vulovic, I.M., Daggett, V. New Dynamic Rotamer Libraries: Data-Driven Analysis of Side Chain Conformational Propensities.\u00a0<b>Structure<\/b>, 24(1):187-199, 2016. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.str.2015.10.017\">DOI<\/a>]<\/li>\n<li>Towse, C.-L., Daggett, V. Modeling protein folding pathways.\u00a0<b>Rev Comput Chem<\/b>, 87-135, 2015. [<a href=\"https:\/\/doi.org\/10.1002\/9781118889886.ch3\">DOI<\/a>]<\/li>\n<li>Towse, C.-L., Hopping, G., Vulovic, I., Daggett, V. Nature versus design: The conformational propensities of D-amino acids and the importance of side chain chirality.\u00a0<b>Protein Engineering, Design, and Selection\u00a0<\/b><i>27\u00a0<\/i>: 447-455, 2014. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzu037\">DOI<\/a>]<\/li>\n<li>Rysavy, S.J., Beck, D.A.C., Daggett, V. Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.\u00a0<b>Protein Science\u00a0<\/b><i>23\u00a0<\/i>: 1584-1595, 2014. [<a href=\"http:\/\/dx.doi.org\/10.1002\/pro.2537\">DOI<\/a>]<\/li>\n<li>Hopping, G., Kellock, J., Barnwal, R.P., Law, P., Bryers, J.D., Varani, G., Caughey, B., Daggett, V. Designed \u03b1-Sheet Peptides Inhibit Amyloid Formation by Targeting Toxic Oligomers.\u00a0<b>eLIFE\u00a0<\/b><i>3:\u00a0<\/i>e01681, 2014. [<a href=\"http:\/\/dx.doi.org\/10.7554\/eLife.01681\">DOI<\/a>]<\/li>\n<li>Merkley, E.D., Rysavy, S., Kahraman, A., Hafen, R.P., Daggett, V., Adkins, J.N. Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances.\u00a0<b>Protein Science\u00a0<\/b><i>23:\u00a0<\/i>747-759, 2014. [<a href=\"http:\/\/dx.doi.org\/10.1002\/pro.2458\">DOI<\/a>]<\/li>\n<li>Cheng, C.J., Daggett, V. Different misfolding mechanisms converge on common conformational changes: Human prion protein pathogenic mutants Y218N and E196K.\u00a0<b>Prion\u00a0<\/b><i>8:<\/i>\u00a01-11, 2014. [<a href=\"http:\/\/dx.doi.org\/10.4161\/pri.27807\">DOI<\/a>]\u00a0<a href=\"http:\/\/depts.washington.edu\/daglab\/downloads\/Prion_Cover.jpg\" data-featherlight=\"image\" aria-hidden=\"true\">[Cover Image]<\/a><\/li>\n<li>Cheng, C.J., Daggett, V. Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH.\u00a0<b>Biomolecules\u00a0<\/b><i>4:<\/i>\u00a0181-201, 2014. [<a href=\"http:\/\/dx.doi.org\/10.3390\/biom4010181\">DOI<\/a>]<\/li>\n<li>Rysavy, S.J., Bromley, D., Daggett, V. DIVE: A graph-based visual analytics framework for big data.\u00a0<b>IEEE Computer Graphics and Applications: Visual Analytics for Biological Data\u00a0<\/b>,\u00a0<i>March\/April<\/i>: 26-37, 2014. [<a href=\"http:\/\/doi.ieeecomputersociety.org\/10.1109\/MCG.2014.27\">DOI<\/a>]<\/li>\n<li>Chen, W., van der Kamp, M.W., Daggett, V. Structural and dynamic properties of the human prion protein.\u00a0<b>Biophysical Journal\u00a0<\/b><i>106:<\/i>\u00a01152-1163, 2014. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2013.12.053\">DOI<\/a>]<\/li>\n<li>Bromley, D., Rysavy, S.J., Su, R., Toofanny, R.D., Schmidlin, T., Daggett, V. DIVE: A data intensive visualization engine.\u00a0<b>Bioinformatics\u00a0<\/b>,\u00a0<i>30:<\/i>\u00a0593-595, 2014. [<a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btt721\">DOI<\/a>]<\/li>\n<li>Hopping, G., Kellock, J., Caughey, B., Daggett, V. The designed trpzip-3 beta-hairpin inhibits amyloid formation in two different amyloid systems.\u00a0<b>ACS Medicinal Chemistry Letters\u00a0<\/b>,\u00a0<i>4:<\/i>\u00a0824-828, 2013. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ml300478w\">DOI<\/a>]<\/li>\n<li>Bromley, D., Anderson, P.C., Daggett, V. Structural consequences of mutations to the alpha-tocopherol transfer protein associated with the neurodegenerative diseae ataxia with vitamin E deficiency.\u00a0<b>Biochemistry\u00a0<\/b>,\u00a0<i>52:<\/i>\u00a04264-4273, 2013. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1021\/bi4001084\">DOI<\/a>]<\/li>\n<li>Schmidlin, T., Ploeger, K., Jonsson, A.L. Daggett, V. Early steps in thermal unfolding of superoxide dismutase 1 are similar to the conformational changes associated with the ALS-associated A4V mutation.\u00a0<b>Protein Engineering, Design and Selection<\/b>,\u00a0<i>26:<\/i>\u00a0503-513, 2013. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzt030\">DOI<\/a>]<\/li>\n<li>Wang, D., McCully, M.E., Luo, Z., McMichael, J., Tu, A., Daggett, V., Regnier, M. Structural and function consequences of cardiac tropinin C L57Q and I61Q Ca2+-desensitizing variants.\u00a0<b>Archives of Biochemistry and Biophysics<\/b>,\u00a0<i>535:<\/i>\u00a068-75, 2013. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.abb.2013.02.006\">DOI<\/a>]<\/li>\n<li>Rizzuti, B., Daggett V. Using simulations to provide the framework for experimental protein folding studies.\u00a0<b>Archives of Biochemistry and Biophysics<\/b>,\u00a0<i>531:<\/i>\u00a0128-135, 2013. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.abb.2012.12.015\">DOI<\/a>]<\/li>\n<li>McCully M.E., Beck D.A.C., Daggett V. Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain.\u00a0<b>Protein Engineering, Design &amp; Selection<\/b>,\u00a0<i>26<\/i>:35-45, 2013. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzs063\">DOI<\/a>]<\/li>\n<li>Towse C.L., Daggett V. When a domain is not a domain, and why it is important to properly filter proteins in databases.\u00a0<b>BioEssays<\/b>,\u00a0<i>34<\/i>:1060-1069, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1002\/bies.201200116\">DOI<\/a>]\u00a0<a href=\"http:\/\/depts.washington.edu\/daglab\/downloads\/Bioessays_Cover.gif\" data-featherlight=\"image\" aria-hidden=\"true\">[Cover Image]<\/a><\/li>\n<li>McCully M.E., Beck D.A.C., Daggett V. Multimolecule test-tube simulations of protein unfolding and aggregation.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>,\u00a0<i>109<\/i>:17851-17856 2012. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.1201809109\">DOI<\/a>]<\/li>\n<li>Wang D., Robertson I.M., Li M.X., McCully M.E., Crane M.L., Luo Z., Tu A.Y., Daggett V., Sykes B.D., Regnier M. Structural and functional consequences of the cardiac troponin C L48Q Ca<sup>2+<\/sup>-sensitizing mutation.\u00a0<b>Biochemistry<\/b>,\u00a0<i>51<\/i>: 4473-4487, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi3003007\">DOI<\/a>]<\/li>\n<li>Benson N.C. and Daggett V. A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations.\u00a0<b>Journal of Physical Chemistry B<\/b>,\u00a0<i>116<\/i>:8722-8731, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1021\/jp302103t\">DOI<\/a>]<\/li>\n<li>McCully M.E. and Daggett V. Folding and Dynamics of Engineered Proteins. In\u00a0<b>Protein Engineering Handbook<\/b>, vol. III. Eds. Lutz S and Bornscheuer UT. Wiley-VCH, Weinheim. Chapter 5: Folding and Dynamics of Engineered Proteins, 89-114, 2012.<\/li>\n<li>Benson N.C. and Daggett V. Wavelet Analysis of Protein Motion.\u00a0<b>International Journal of Wavelets, Multiresolution and Information Processing<\/b>,\u00a0<i>10<\/i>:1250040, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1142\/S0219691312500403\">DOI<\/a>]<\/li>\n<li>Towse C.L. and Daggett V. Molecular Dynamics Simulations. In\u00a0<b>Encyclopedia of Biophysics<\/b>, Springer,\u00a0<i>In Press<\/i>, 2012.<\/li>\n<li>Scouras A.D. and Daggett V. Disruption of the X-Loop Turn of the Prion Protein Linked to Scrapie Resistance.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>25<\/i>: 243-249, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzs009\">DOI<\/a>] [\u00a0<a href=\"http:\/\/peds.oxfordjournals.org\/content\/25\/5.cover-expansion\">Cover Image<\/a>]<\/li>\n<li>Benson N.C. and Daggett V. A Chemical Group Graph Representation for Efficient High-Throughput Analysis of Atomistic Protein Simulations.\u00a0<b>Journal of Bioinformatics and Computational Biology<\/b>\u00a0<i>10<\/i>:1250008-1250024, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1142\/S0219720012500084\">DOI<\/a>]<\/li>\n<li>Toofanny R.D. and Daggett V. Understanding protein unfolding from molecular simulations.\u00a0<b>WIREs Computational Molecular Science<\/b>\u00a0<i>2<\/i>:405-423, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1002\/wcms.1088\">DOI<\/a>]<\/li>\n<li>Merkley E.D., Daggett V., and Parson W.W. A temperature-dependent conformational change of NADH oxidase from\u00a0<i>Thermus thermophilus<\/i>\u00a0HB8.\u00a0<b>Proteins: Structure, Function, and Bioinformatics<\/b>\u00a0<i>80<\/i>:546-555, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1002\/prot.23219\">DOI<\/a>]<\/li>\n<li>Simms A.M. and Daggett V. Protein simulation data in the relational model.\u00a0<b>The Journal of Supercomputing<\/b>,\u00a0<i>62<\/i>:150-173, 2012. [<a href=\"http:\/\/dx.doi.org\/10.1007\/s11227-011-0692-3\">DOI<\/a>]<\/li>\n<li>Morrone A., Giri R., Toofanny R.D., Travaglini-Allocatelli C., Brunori M., Daggett V., and Gianni S. GB1 Is Not a Two-State Folder: Identification and Characterization of an On-Pathway Intermediate.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>101<\/i>:2053-2060, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2011.09.013\">DOI<\/a>]<\/li>\n<li>Jonsson A.L. and Daggett V. The Effect of Context on the Folding of \u03b2-Hairpins.\u00a0<b>Journal of Structural Biology<\/b>\u00a0<i>176<\/i>:143-150, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jsb.2011.08.001\">DOI<\/a>]<\/li>\n<li>Toofanny R.D., Simms A.M., Beck D.A.C., and Daggett V. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.\u00a0<b>BMC Bioinformatics<\/b>\u00a0<i>12<\/i>:334, 2011. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1186\/1471-2105-12-334\">DOI<\/a>]<\/li>\n<li>Calhoun S. and Daggett V. Structural effects of the L145Q, V157F, and R282W cancer-associated mutations in the p53 DNA-binding core domain.\u00a0<b>Biochemistry<\/b>\u00a0<i>50<\/i>:5345-5353, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi200192j\">DOI<\/a>]<\/li>\n<li>Van der Kamp M.W. and Daggett V. Molecular Dynamics as an Approach to Study Prion Protein Misfolding and the Effect of Pathogenic Mutations.\u00a0<b>Topics in Current Chemistry<\/b>\u00a0<i>305<\/i>:169-197, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1007\/128_2011_158\">DOI<\/a>]<\/li>\n<li>Banachewicz W., Religa T.L., Schaeffer R.D., Daggett V., and Fersht A.R. Malleability of folding intermediates in the homeodomain superfamily.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>108<\/i>:5596-5601, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.1101752108\">DOI<\/a>]<\/li>\n<li>Dar T.A., Schaeffer R.D., Daggett V., and Bowler B.E. Manifestations of Native Topology in the Denatured State Ensemble of\u00a0<i>Rhodopseudomonas palustris<\/i>\u00a0Cytochrome\u00a0<i>c<\/i>\u2032.\u00a0<b>Biochemistry<\/b>\u00a0<i>50<\/i>:1029-1041, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi101551h\">DOI<\/a>]<\/li>\n<li>Scouras A.D. and Daggett V. The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water.\u00a0<b>Protein Science<\/b>\u00a0<i>20<\/i>:341-352, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1002\/pro.565\">DOI<\/a>]\n<ul>\n<li>Research Highlight on this paper in\u00a0<b>Protein Science<\/b>. [<a href=\"http:\/\/dx.doi.org\/10.1002\/pro.586\">DOI<\/a>]<\/li>\n<\/ul>\n<\/li>\n<li>Morrone A., McCully M.E., Bryan P.N., Brunori M., Daggett V., Gianni S., Travaglini-Allocatelli C. The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function.\u00a0<b>The Journal of Biological Chemistry<\/b>\u00a0<i>286<\/i>:3863-3872, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1074\/jbc.M110.155911\">DOI<\/a>]<\/li>\n<li>Schaeffer R.D, Jonsson A.L., Simms A.M., and Daggett V. Generation of a Consensus Protein Domain Dictionary.\u00a0<b>Bioinformatics<\/b>\u00a0<i>27<\/i>:46-54, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btq625\">DOI<\/a>]<\/li>\n<li>Schaeffer R.D. and Daggett V. Protein folds and protein folding.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>24<\/i>:11-19, 2011. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzq096\">DOI<\/a>]<\/li>\n<li>Jonsson A.L., Schaeffer R.D., van der Kamp M.W., and Daggett V. Dynameomics: protein dynamics and unfolding across fold space.\u00a0<b>Biomolecular Concepts<\/b>\u00a0<i>1<\/i>:335-344, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1515\/BMC.2010.032\">DOI<\/a>]<\/li>\n<li>Chen W., Van der Kamp M.W., and Daggett V. Diverse Effects on the Native \u03b2-Sheet of the Human Prion Protein Due to Disease-Associated Mutations.\u00a0<b>Biochemistry<\/b>\u00a0<i>49<\/i>:9874-9881, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi101449f\">DOI<\/a>]<\/li>\n<li>Van der Kamp M.W. and Daggett V. Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>404<\/i>:732-748, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2010.09.060\">DOI<\/a>][\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2994014\/?tool=pubmed\">HTML<\/a>]<\/li>\n<li>Van der Kamp M.W. and Daggett V. The influence of pH on the human prion protein: Insights into the early steps of misfolding.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>99<\/i>:2289-2298, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2010.07.063\">DOI<\/a>]<\/li>\n<li>McCully M.E., Beck D.A.C., Fersht A.R., and Daggett V. Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>99<\/i>:1628-1636, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2010.06.040\">DOI<\/a>]<\/li>\n<li>Toofanny R.D., Jonsson A.L., and Daggett V. A Comprehensive Multidimensional-Embedded, One-Dimensional Reaction Coordinate for Protein Unfolding\/Folding.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>98<\/i>:2671-2681, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2010.02.048\">DOI<\/a>]<\/li>\n<li>Rutherford K. and Daggett V. Polymorphisms and disease: hotspots of inactivation in methyltransferases.\u00a0<b>Trends in Biochemical Sciences<\/b>\u00a0<i>35<\/i>:531-538, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.tibs.2010.03.007\">DOI<\/a>]<\/li>\n<li>Van der Kamp M.W., Schaeffer R.D., Jonsson A.L., Scouras A.D., Simms A.M., Toofanny R.D., Benson N.C., Anderson P.C., Merkley E.D., Rysavy S., Bromley D., Beck D.A.C., and Daggett V. Dynameomics: A Comprehensive Database of Protein Dynamics.\u00a0<b>Structure<\/b>\u00a0<i>18<\/i>:423-435, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.str.2010.01.012\">DOI<\/a>] [<a href=\"http:\/\/download.cell.com\/images\/journalimages\/0969-2126\/S0969212610X00053_covhighres.jpg\" data-featherlight=\"image\" aria-hidden=\"true\">Cover Image<\/a>]\n<ul>\n<li>Research Highlight on this paper in\u00a0<b>Nature Methods<\/b>. [<a href=\"http:\/\/dx.doi.org\/10.1038\/nmeth0610-426\">DOI<\/a>]<\/li>\n<\/ul>\n<\/li>\n<li>Merkley E.D., Parson W.W., and Daggett V. Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>23<\/i>:327-336, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzp090\">DOI<\/a>] [<a href=\"http:\/\/peds.oxfordjournals.org\/cgi\/data\/gzp090\/DC1\/1\">Color Figures<\/a>]<\/li>\n<li>Law P.B. and Daggett V. The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>23<\/i>: 27-33, 2010. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzp069\">DOI<\/a>]<\/li>\n<li>Key J., Scheuermann T.H., Anderson P.C., Daggett V., and Gardner K.H. Principles of Ligand Binding within a Completely Buried Cavity in HIF2\u03b1 PAS-B.\u00a0<b>Journal of the American Chemical Society<\/b>\u00a0<i>131<\/i>: 17647-17654, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ja9073062\">DOI<\/a>] [<a href=\"http:\/\/pubs.acs.org\/doi\/full\/10.1021\/ja9073062\">HTML<\/a>]<\/li>\n<li>Jonsson A.L., Scott K.A., and Daggett V. Dynameomics: A consensus view of the protein unfolding\/folding transition state ensemble across a diverse set of protein folds.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>97<\/i>: 2958-2966, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2009.09.012\">DOI<\/a>]<\/li>\n<li>Rutherford K. and Daggett V. The V119I Polymorphism in Protein\u00a0<i>L<\/i>-Isoaspartate\u00a0<i>O<\/i>-Methyltransferase Alters the Substrate-Binding Interface.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>22<\/i>: 713-721, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzp056\">DOI<\/a>] [<a href=\"http:\/\/peds.oxfordjournals.org\/cgi\/data\/gzp056\/DC1\/1\">Color Figures<\/a>]<\/li>\n<li>Daggett V. Shedding light on amyloidosis with protein engineering.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>22<\/i>: 445, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzp049\">DOI<\/a>]<\/li>\n<li>Van der Kamp M.W. and Daggett V. The consequences of pathogenic mutations to the human prion protein.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>22<\/i>: 461-468, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzp039\">DOI<\/a>] [<a href=\"http:\/\/peds.oxfordjournals.org\/cgi\/data\/gzp039\/DC1\/1\">Color Figures<\/a>]<\/li>\n<li>Schmidlin T., Kennedy B., and Daggett V. Structural changes to monomeric CuZn Superoxide Dismutase caused by the familial Amyotrophic Lateral Sclerosis mutation A4V.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>97<\/i>: 1709-1718, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bpj.2009.06.043\">DOI<\/a>]<\/li>\n<li>Anderson P.C. and Daggett V. The R46Q, R131Q and R154H Polymorphs of Human DNA Glycosylase\/\u03b2-Lyase hOgg1 Severely Distort the Active Site and DNA Recognition Site but do not Cause Unfolding.\u00a0<b>Journal of the American Chemical Society<\/b>\u00a0<i>131<\/i>: 9506-9515, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ja809726e\">DOI<\/a>]<\/li>\n<li>Rutherford K. and Daggett V. A Hotspot of Inactivation: The A22S and V108M Polymorphisms Individually Destabilize the Active Site Structure of Catechol\u00a0<i>O<\/i>-Methyltransferase.\u00a0<b>Biochemistry<\/b>\u00a0<i>48<\/i>: 6450-6460, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi900174v\">DOI<\/a>]<\/li>\n<li>Daggett V. and Fersht A.R. Protein folding and binding: moving into unchartered territory.\u00a0<b>Current Opinion in Structural Biology<\/b>\u00a0<i>19<\/i>: 1-2, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.sbi.2009.01.006\">DOI<\/a>]<\/li>\n<li>DeMarco M.L. and Daggett V. Characterization of cell-surface prion protein relative to its recombinant analogue: Insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein.\u00a0<b>Journal of Neurochemistry<\/b>\u00a0<i>109<\/i>: 60-73, 2009. [<a href=\"http:\/\/dx.doi.org\/10.1111\/j.1471-4159.2009.05892.x\">DOI<\/a>]<\/li>\n<li>Benson N. and Daggett V. Dynameomics: Large-Scale Assessment of Native Protein Flexibility.\u00a0<b>Protein Science<\/b>\u00a0<i>17<\/i>: 2038-2050, 2008.[<a href=\"http:\/\/dx.doi.org\/10.1110\/ps.037473.108\">DOI<\/a>]<\/li>\n<li>Anderson P.C. and Daggett V. Molecular Basis for the Structural Instability of Human DJ-1 Induced by the L166P Mutation Associated with Parkinson\u2019s Disease.\u00a0<b>Biochemistry<\/b>\u00a0<i>47<\/i>: 9380-9393, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi800677k\">DOI<\/a>]<\/li>\n<li>Beck D.A.C., Alonso D.O.V., Inoyama D., and Daggett V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>105<\/i>: 12259-12264, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0706527105\">DOI<\/a>]<\/li>\n<li>Rutherford K., Alphand\u00e9ry E., McMillan A., Daggett V., and Parson W.W. The V108M mutation decreases the structural stability of catechol\u00a0<i>O<\/i>-methyltransferase.\u00a0<b>Biochimica et Biophysica Acta<\/b>\u00a0<i>1784<\/i>: 1098-1105, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.bbapap.2008.04.006\">DOI<\/a>]<\/li>\n<li>McCully M.E., Beck D.A.C., and Daggett V. Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain.\u00a0<b>Biochemistry<\/b>\u00a0<i>47<\/i>: 7079-7089, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi800118b\">DOI<\/a>]<\/li>\n<li>Smolin N., Li B., Beck D.A.C., and Daggett V. Side-chain dynamics are critical for water permeation through aquaporin-1.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>95<\/i>: 1089-1098, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1529\/biophysj.107.125187\">DOI<\/a>]<\/li>\n<li>Rutherford K. and Daggett V. Four Human Thiopurine S-Methyltransferase Alleles Severely Affect Protein Structure and Dynamics.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>379<\/i>: 803-814, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2008.04.032\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2518407\/?tool=pubmed\">HTML<\/a>]<\/li>\n<li>Kehl C., Simms A.M., Toofanny R.D., and Daggett V. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>21<\/i>: 379-386, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzn015\">DOI<\/a>]<\/li>\n<li>Simms A.M., Toofanny R.D., Kehl C., Benson N.C., and Daggett V. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>21<\/i>: 369-377, 2008. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzn012\">DOI<\/a>]<\/li>\n<li>Beck D.A.C., Jonsson A.L., Schaeffer R.D., Scott K.A., Day R., Toofanny R.D., Alonso D.O.V., and Daggett V. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations.\u00a0<b>Protein Engineering Design &amp; Selection<\/b>\u00a0<i>21<\/i>: 353-368, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzn011\">DOI<\/a>]<\/li>\n<li>Scouras A.D. and Daggett V. Species variation in PrP<sup>Sc<\/sup>\u00a0protofibril models.\u00a0<b>Journal of Materials Science<\/b>\u00a0<i>43<\/i>: 3625-3637, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1007\/s10853-008-2578-1\">DOI<\/a>]<\/li>\n<li>Smolin N. and Daggett V. Formation of ice-like water structure on the surface of an antifreeze protein.\u00a0<b>Journal of Physical Chemistry B<\/b>\u00a0<i>112<\/i>: 6193-6206, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1021\/jp710546e\">DOI<\/a>]<\/li>\n<li>Steward R.E., Armen R.S., and Daggett V. Different disease-causing mutations in transthyretin trigger the same conformational conversion.\u00a0<b>Protein Engineering, Design &amp; Selection<\/b>\u00a0<i>21<\/i>: 187-195, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1093\/protein\/gzm086\">DOI<\/a>]<\/li>\n<li>Schaeffer R.D., Fersht A.R., and Daggett V. Combining experiment and simulation in protein folding: closing the gap for small model systems.\u00a0<b>Current Opinion in Structural Biology<\/b>\u00a0<i>18<\/i>: 4-9, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.sbi.2007.11.007\">DOI<\/a>]<\/li>\n<li>Rutherford K., Parson W.W., and Daggett V. The Histamine\u00a0<i>N<\/i>-Methyltransferase T105I Polymorphism Affects Active Site Structure and Dynamics.\u00a0<b>Biochemistry<\/b>\u00a0<i>47<\/i>: 893-901, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi701737f\">DOI<\/a>]<\/li>\n<li>Merkley E.D., Bernard B., and Daggett V. Conformational Changes below the\u00a0<i>T<\/i><sub>m<\/sub>: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A.\u00a0<b>Biochemistry<\/b>\u00a0<i>47<\/i>: 880-892, 2008. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi701565b\">DOI<\/a>]<\/li>\n<li>Beck D.A.C. and Daggett V. A One-Dimensional Reaction Coordinate for Identification of Transition States from Explicit Solvent\u00a0<i>P<\/i><sub>fold<\/sub>-Like Calculations.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>93<\/i>: 3382-3391, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1529\/biophysj.106.100149\">DOI<\/a>]<\/li>\n<li>Beck D.A.C., Bennion B.J., Alonso D.O.V., and Daggett V. Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics.\u00a0<b>Methods in Enzymology<\/b>\u00a0<i>428<\/i>: 373-396, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0076-6879(07)28022-X\">DOI<\/a>]<\/li>\n<li>Sharpe T., Jonsson A.L., Rutherford T.J., Daggett V., and Fersht A.R. The role of the turn in \u03b2-hairpin formation during WW domain folding.\u00a0<b>Protein Science<\/b>\u00a0<i>16<\/i>: 2233-2239, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1110\/ps.073004907\">DOI<\/a>]<\/li>\n<li>Beck D.A.C., White G.W.N., and Daggett V. Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.\u00a0<b>Journal of Structural Biology<\/b>\u00a0<i>157<\/i>: 514-523, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jsb.2006.10.002\">DOI<\/a>]<\/li>\n<li>Fersht A.R. and Daggett V. Folding and binding: implementing the game plan.\u00a0<b>Current Opinion in Structural Biology<\/b>\u00a0<i>17<\/i>: 1-2, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.sbi.2007.01.011\">DOI<\/a>]<\/li>\n<li>Day R. and Daggett V. Direct Observation of Microscopic Reversibility in Single-molecule Protein Folding.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>366<\/i>: 677-686, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2006.11.043\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1885941\/\">HTML<\/a>]<\/li>\n<li>Scott K.A. and Daggett V. Folding mechanisms of proteins with high sequence identity but different folds.\u00a0<b>Biochemistry<\/b>\u00a0<i>46<\/i>: 1545-1556, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi061904l\">DOI<\/a>]<\/li>\n<li>Scott K.A., Alonso D.O.V., Sato S., Fersht A.R., and Daggett V. Conformational Entropy of Alanine versus Glycine in Protein Denatured States.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>104<\/i>: 2661-2666, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0611182104\">DOI<\/a>]<\/li>\n<li>DeMarco M.L. and Daggett V. Molecular Mechanism for Low pH-Triggered Misfolding of the Human Prion Protein.\u00a0<b>Biochemistry<\/b><i>46<\/i>: 3045-3054, 2007. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi0619066\">DOI<\/a>]<\/li>\n<li>DeMarco M.L., Silveira J., Caughey B., and Daggett V. Structural Properties of Prion Protein Protofibrils and Fibrils: An Experimental Assessment of Atomic Models.\u00a0<b>Biochemistry<\/b>\u00a0<i>45<\/i>: 15573-15582, 2006. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi0612723\">DOI<\/a>]<\/li>\n<li>Petrovich M., Jonsson A.L., Ferguson N., Daggett V., and Fersht A.R. \u03a6-Analysis at the Experimental Limits: Mechanism of \u03b2-Hairpin Formation.<b>\u00a0Journal of Molecular Biology<\/b>\u00a0<i>360<\/i>: 865-881, 2006. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2006.05.050\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16784750\">HTML<\/a>]<\/li>\n<li>Daggett V. \u03b1-Sheet: The toxic conformer in amyloid diseases?<b>\u00a0Accounts of Chemical Research<\/b>\u00a0<i>39<\/i>: 594-602, 2006. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ar0500719\">DOI<\/a>]<\/li>\n<li>Daggett V. Protein Folding-Simulation.\u00a0<b>Chemical Reviews<\/b>\u00a0<i>106<\/i>: 1898-1916, 2006. [<a href=\"http:\/\/dx.doi.org\/10.1021\/cr0404242\">DOI<\/a>]<\/li>\n<li>Scott K.A., Randles L.G., Moran S.J., Daggett V., and Clarke J. The Folding Pathway of Spectrin R17 from Experiment and Simulations: Using Experimentally Validated MD Simulations to Characterize States Hinted at by Experiment.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>359<\/i>: 159-173, 2006. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2006.03.011\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16618492\">HTML<\/a>]<\/li>\n<li>Scott K.A., Alonso D.O.V., Pan Y., and Daggett V. Importance of Context in Protein Folding: Secondary Structural Propensities versus Tertiary Contact-Assisted Secondary Structure Formation.\u00a0<b>Biochemistry<\/b>\u00a0<i>45<\/i>: 4153-4163, 2006. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi0517281\">DOI<\/a>]<\/li>\n<li>Rutherford K., Bennion B.J., Parson W.W., and Daggett V. The 108M Polymorph of Human Catechol\u00a0<i>O<\/i>-Methyltransferase Is Prone to Deformation at Physiological Temperatures.\u00a0<b>Biochemistry<\/b>\u00a0<i>45<\/i>: 2178-2188, 2006. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi051988i\">DOI<\/a>]<\/li>\n<li>Armen R.S. and Daggett V. Characterization of Two Distinct \u03b2<sub>2<\/sub>-Microglobulin Unfolding Intermediates that May Lead to Amyloid Fibrils of Different Morphology.\u00a0<b>Biochemistry<\/b>\u00a0<i>44<\/i>: 16098-16107, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi050731h\">DOI<\/a>]<\/li>\n<li>Armen R.S., Bernard B.M., Day R, Alonso D.O.V., and Daggett V. Characterization of a possible amyloidogenic precursor in glutamine-repeat diseases.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>102<\/i>: 13433-13438, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0502068102\">DOI<\/a>]<\/li>\n<li>Day R. and Daggett V. Ensemble versus single-molecule protein unfolding.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>102<\/i>: 13445-13450, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0501773102\">DOI<\/a>]<\/li>\n<li>DeMarco M.L. and Daggett V. Local environmental effects on the structure of the prion protein.\u00a0<b>Comptes Rendus Biologies<\/b><i>\u00a0238<\/i>: 847-862, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.crvi.2005.05.001\">DOI<\/a>]<\/li>\n<li>Beck D.A.C., Armen R.S., and Daggett V. Cutoff size need not strongly influence molecular dynamics results on solvated polypeptides.\u00a0<b>Biochemistry<\/b>\u00a0<i>44<\/i>: 609-616, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi0486381\">DOI<\/a>]<\/li>\n<li>Esposito L. and Daggett V. Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations.\u00a0<b>Biochemistry<\/b>\u00a0<i>44<\/i>: 3358-3368, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi0488350\">DOI<\/a>]<\/li>\n<li>Jemth P., Day R., Gianni S., Khan F., Allen M., Daggett V., and Fersht A.R. The structure of the major transition state for folding of an FF domain from experiment and simulation.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>350<\/i>: 363-378, 2005. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2005.04.067\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15935381\">HTML<\/a>]<\/li>\n<li>Ferguson N., Day R., Johnson C.M., Allen M.D., Daggett V., and Fersht A.R. Simulation and experiment at high temperatures: Ultrafast folding of a thermophilic protein by nucleation-condensation.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>347<\/i>: 855-870, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2004.12.061\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15769475\">HTML<\/a>]<\/li>\n<li>White G.W.N., Gianni S., Grossman J.G., Jemth P., Fersht A.R., and Daggett V. Simulation and Experiment Conspire to reveal Cryptic Intermediates and the Slide from the Nucleation-Condensation to Framework Mechanism of Folding.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>350<\/i>: 757-775, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2005.05.005\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15967458\">HTML<\/a>]<\/li>\n<li>Day R. and Daggett v. Sensitivity of the folding\/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent.\u00a0<b>Protein Science<\/b>\u00a0<i>14<\/i>: 1242-1252, 2005. [<a href=\"http:\/\/dx.doi.org\/10.1110\/ps.041226005\">DOI<\/a>]<\/li>\n<li>Armen R.S., DeMarco M.L., Alonso D.O.V., and Daggett V. Pauling and Corey\u2019s \u03b1-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>101<\/i>: 11622-11627, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0401781101\">DOI<\/a>]\n<ul>\n<li>Editorial on this paper in\u00a0<b>Nature<\/b>. [<a href=\"http:\/\/dx.doi.org\/10.1038\/430739a\">DOI<\/a>]<\/li>\n<li>Editorial on this paper in\u00a0<b>Science<\/b>. [<a href=\"http:\/\/www.sciencemag.org\/cgi\/reprint\/305\/5690\/1535c.pdf\">PDF<\/a>] [<a href=\"http:\/\/www.sciencemag.org\/content\/vol305\/issue5690\/twil.dtl#305\/5690\/1535b\">HTML<\/a>]<\/li>\n<\/ul>\n<\/li>\n<li>Armen R.S., Alonso D.O.V., and Daggett V. Anatomy of an amyloidogenic intermediate: Conversion of \u03b2-sheet to \u03b1-pleated sheet structure in transthyretin at acidic pH.\u00a0<b>Structure<\/b>\u00a0<i>12<\/i>: 1847-1863, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.str.2004.08.005\">DOI<\/a>]<\/li>\n<li>Rizzuti B., Daggett V., Guzzi R., and Sportelli L. The early steps in the unfolding of azurin.\u00a0<b>Biochemistry<\/b>\u00a0<i>43<\/i>: 15604-15609. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi048685t\">DOI<\/a>]<\/li>\n<li>Bennion B.J., DeMarco M.L., and Daggett V. Preventing misfolding of the prion protein by Trimethylamine\u00a0<i>N<\/i>-oxide.\u00a0<b>Biochemistry<\/b>\u00a0<i>4<\/i>1, 12955-12963, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi0486379\">DOI<\/a>]<\/li>\n<li>DeMarco M.L., Alonso D.O.V., and Daggett V. Diffusing and colliding: The atomic level folding\/unfolding pathway of a small helical protein.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>341<\/i>: 1109-1124, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2004.06.074\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15328620\">HTML<\/a>]<\/li>\n<li>Beck D.A.C. and Daggett V. Methods for Molecular Dynamics Simulations of Protein Folding\/Unfolding in Solution.\u00a0<b>Methods<\/b>\u00a0<i>34<\/i>: 112-120, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1016\/j.ymeth.2004.03.008\">DOI<\/a>]<\/li>\n<li>Bennion B.J. and Daggett V. Counteraction of urea-induced protein denaturation by trimethylamine\u00a0<i>N<\/i>-oxide: A chemical chaperone at atomic resolution.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>101<\/i>: 6433-6438, 2004. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0308633101\">DOI<\/a>]<\/li>\n<li>Sato S., Religa T., Daggett V., and Fersht A.R. Testing protein-folding simulations by experiment: B domain of protein A.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0101, 6952-6956, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0401396101\">DOI<\/a>]<\/li>\n<li>Jemth P., Gianni S., Day R., Li B., Johnson C.M., Daggett V., and Fersht A.R. Demonstration of a low energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>101<\/i>: 6450-6455, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0401732101\">DOI<\/a>]<\/li>\n<li>DeMarco M.L. and Daggett V. From Conversion to Aggregation: Protofibril Formation of the Prion Protein.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>101<\/i>: 2293-2298, 2004. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0307178101\">DOI<\/a>]<\/li>\n<li>Zhu Y., Alonso D.O.V., Maki K., Huang C.-Y., Lahr S.J., Daggett V., Roder H., DeGrado W.F., and Gai F. Ultrafast folding of \u03b1<sub>3<\/sub>D, A\u00a0<i>de novo<\/i>\u00a0designed three-helix bundle protein.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>100<\/i>:15486-15491, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.2136623100\">DOI<\/a>]<\/li>\n<li>Gianni S., Guydosh N.R., Khan F., Caldas T.D. Mayor U., White G.W.N., DeMarco M.L., Daggett V., and Fersht A.R. Unifying features in protein folding mechanisms.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>100<\/i>: 13286-13291, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.1835776100\">DOI<\/a>]<\/li>\n<li>Day R., Beck D.A.C., Armen R. and Daggett V. A Consensus View of Fold Space: Combining SCOP, CATH, and the Dali Domain Dictionary.\u00a0<b>Protein Science<\/b>\u00a0<i>12<\/i>: 2150-2160, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1110\/ps.0306803\">DOI<\/a>]<\/li>\n<li>Daggett V. and Fersht A.R. The present view of the mechanism of protein folding.\u00a0<b>Nature Reviews: Molecular Cell Biology<\/b>\u00a0<i>4<\/i>: 497-502, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1038\/nrm1126\">DOI<\/a>]<\/li>\n<li>Mayor M., Guydosh N.R., Johnson C.M., Grossmann J.G., Sato S., Jas G.S., Freund S.M.V., Alonso D.O.V., Daggett V. and Fersht A.R. The complete folding pathway of a protein from nanoseconds to microseconds.\u00a0<b>Nature<\/b>\u00a0<i>421<\/i>: 863-867, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1038\/nature01428\">DOI<\/a>]<\/li>\n<li>Day R. and Daggett V. All-atom simulations of protein folding and unfolding. In \u201cProtein Simulations,\u201d V. Daggett, Editor.\u00a0<b>Advances in Protein Chemistry<\/b>\u00a0<i>66<\/i>: 373-403, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0065-3233(03)66009-2\">DOI<\/a>]<\/li>\n<li>Beck D.A.C., Alonso D.O.V., and Daggett V. A microscopic view of peptide and protein solvation.\u00a0<b>Biophysical Chemistry<\/b>\u00a0<i>100<\/i>: 221-237, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0301-4622(02)00283-1\">DOI<\/a>]<\/li>\n<li>Armen R., Alonso D.O.V., and Daggett V. The Role of \u03b1-, 3<sub>10<\/sub>-, and \u03c0-helix in Helix \u2192 Coil Transitions.\u00a0<b>Protein Science<\/b>\u00a0<i>12<\/i>: 1145-1157, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1110\/ps.0240103\">DOI<\/a>]<\/li>\n<li>Bennion B.J. and Daggett V. The molecular basis for the chemical denaturation of proteins by urea.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>100<\/i>: 5142-5147, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.0930122100\">DOI<\/a>]<\/li>\n<li>Walsh S.T.R., Cheng R.P., Alonso D.O.V., Daggett V., Vanderkooi J., and DeGrado W.F. The Hydration of Amides in Helices; A Comprehensive Picture from Molecular Dynamics, IR and NMR.\u00a0<b>Protein Science<\/b>\u00a0<i>12<\/i>: 520-531, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1110\/ps.0223003\">DOI<\/a>] [<a href=\"http:\/\/www3.interscience.wiley.com\/journal\/121602069\/abstract\">HTML<\/a>]<\/li>\n<li>Li B. and Daggett V. The Molecular Basis for the Extensibility of Elastin.\u00a0<b>Journal of Muscle Research and Cell Motility<\/b>\u00a0<i>23<\/i>: 561-573, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1023\/A:1023474909980\">DOI<\/a>]<\/li>\n<li>Daggett V. and Fersht A.R. Is There a Unifying Mechanism for Protein Folding?\u00a0<b>Trends in Biochemical Sciences<\/b>\u00a0<i>28<\/i>: 18-25, 2003. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0968-0004(02)00012-9\">DOI<\/a>]<\/li>\n<li>Li B. and Daggett V. The molecular basis for temperature- and pH-induced conformational transitions in elastin-based peptides.\u00a0<b>Biopolymers<\/b>\u00a0<i>68<\/i>: 121-129. [<a href=\"http:\/\/dx.doi.org\/10.1002\/bip.10204\">DOI<\/a>]<\/li>\n<li>Bennion B.J. and Daggett V. Protein Conformation and Diagnostic Tests: The Prion Protein.\u00a0<b>Clinical Chemistry<\/b>\u00a0<i>48<\/i>: 2105-2114, 2002. [<a href=\"http:\/\/www.clinchem.org\/cgi\/reprint\/48\/12\/2105.pdf\">PDF<\/a>] [<a href=\"http:\/\/www.clinchem.org\/cgi\/content\/abstract\/48\/12\/2105\">HTML<\/a>]<\/li>\n<li>Day R., Bennion B., Ham S., and Daggett V. Increasing temperature accelerates protein unfolding without changing the pathway of unfolding.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>322<\/i>: 189-203, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0022-2836(02)00672-1\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/12215424\">HTML<\/a>]<\/li>\n<li>Li B., Alonso D.O.V., and Daggett V. Stabilization of globular proteins via introduction of temperature-activated elastin-based switches.\u00a0<b>Structure<\/b>\u00a0<i>10<\/i>: 989-998, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0969-2126(02)00792-X\">DOI<\/a>]<\/li>\n<li>Alonso D.O.V., An C., and Daggett V. Simulations of biomolecules: characterization of the early steps in the pH-induced conformational conversion of the hamster, bovine and human forms of the prion protein.\u00a0<b>Philosophical Transactions of the Royal Society<\/b>\u00a0<i>360<\/i>: 1165-1178, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1098\/rsta.2002.0986\">DOI<\/a>]<\/li>\n<li>De Jong D., Alonso D.O.V., Riley R., and Daggett V. Probing the Energy Landscape of Protein Folding\/Unfolding Transition States.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>319<\/i>: 229-242, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0022-2836(02)00212-7\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/12051948\">HTML<\/a>]<\/li>\n<li>Daggett V. Molecular dynamics simulations of the protein unfolding\/folding reaction.\u00a0<b>Accounts of Chemical Research<\/b>\u00a0<i>35<\/i>: 422-429, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ar0100834\">DOI<\/a>]<\/li>\n<li>Fersht A.R. and Daggett V. Protein Folding and Unfolding at Atomic Resolution.\u00a0<b>Cell<\/b>\u00a0<i>108<\/i>: 573-582, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0092-8674(02)00620-7\">DOI<\/a>]<\/li>\n<li>Zou Q., Bennion B.J., Daggett V., and Murphy K.P. The Molecular Mechanism of Stabilization of Proteins by TMAO and its Ability to Counteract the Effects of Urea.\u00a0<b>Journal of the American Chemical Society<\/b>\u00a0<i>125<\/i>: 1192-1202, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ja004206b\">DOI<\/a>]<\/li>\n<li>Kazmirski S.L., Isaacson R.L., An C., Buckle A., Johnson C.M., Daggett V., and Fersht A.R. Loss of a metal-binding site in gelsolin leads to familial amyloidosis\u2013Finnish type.\u00a0<b>Nature Structural Biology<\/b>\u00a0<i>9<\/i>: 112-116, 2002. [<a href=\"http:\/\/dx.doi.org\/10.1038\/nsb745\">DOI<\/a>]<\/li>\n<li>Li B., Alonso D.O.V., Bennion B.J., and Daggett V. Hydrophobic Hydration is an Important Source of Elasticity in Elastin-Based Biopolymers.\u00a0<b>Journal of the American Chemical Society<\/b>\u00a0<i>123<\/i>: 11991-11998, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ja010363e\">DOI<\/a>]<\/li>\n<li>Ferguson N., Pires J.R., Toepert F., Johnson C.J., Pan Y.P., Volkmer-Engert R., Schneider-Mergener J., Daggett V., Oschkinat H., and Fersht A.R. Using flexible loop mimetics to extend \u03a6-value analysis to secondary structure interactions.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>98<\/i>: 13008-13013, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.221467398\">DOI<\/a>]<\/li>\n<li>Best R.B., Li B., Steward A., Daggett V., and Clarke J. Can non-mechanical proteins withstand force? Stretching barnase by AFM and MD simulation.\u00a0<b>Biophysical Journal<\/b>\u00a0<i>81<\/i>: 2344-2356, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0006-3495(01)75881-X\">DOI<\/a>]<\/li>\n<li>Main E.R.G., Fulton K.F., Daggett V., and Jackson S.E. A Comparison of Experimental and Computational Methods for Mapping the Interactions Present in the Transition State for Folding of FKBP12.\u00a0<b>Journal of Biological Physics<\/b>\u00a0<i>27<\/i>: 99-117, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1023\/A:1013137924581\">DOI<\/a>]<\/li>\n<li>Daggett V. Validation of Protein-Unfolding Transition States Identified in Molecular Dynamics Simulations.\u00a0<i>From Protein Folding to New Enzymes<\/i>. A. Berry and S.E. Radford, Editors.\u00a0<b>Biochemical Society Symposium<\/b>. Portland Press: London,\u00a0<i>68<\/i>: 89-93, 2001. [<a href=\"http:\/\/symposia.biochemistry.org\/bssymp\/068\/bss0680083.htm\">HTML<\/a>]<\/li>\n<li>Ramamurthy V., Tucker C., Wilkie S.E., Daggett V., Hunt D.M. and Hurley J.B. Interactions within the Coiled-coil Domain of RetGC-1 Guanylyl Cyclase are Optimized for Regulation Rather than for High Affinity.\u00a0<b>Journal of Biological Chemistry<\/b>\u00a0<i>276<\/i>: 26218-26229, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1074\/jbc.M010495200\">DOI<\/a>]<\/li>\n<li>Alonso D.O.V. and Daggett V. Simulations and Computational Analyses of Prion Protein Conformations.\u00a0<i>Prion Proteins<\/i>. Byron Caughey, Editor.\u00a0<b>Advances in Protein Chemistry<\/b>. Academic Press: San Diego,\u00a0<i>57<\/i>:107-137, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0065-3233(01)57020-5\">DOI<\/a>]<\/li>\n<li>Alonso D.O.V., DeArmond S., Cohen F.E., and Daggett V. Mapping the early steps of the pH-induced conformational conversion of the prion protein.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>98<\/i>: 2985-2989, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.061555898\">DOI<\/a>]<\/li>\n<li>Kazmirski S.L., Wong K.B., Freund S.M.V., Tan Y.J., Fersht A.R., and Daggett V. Protein Folding from a Highly Disordered Denatured State: The Folding Pathway of Chymotrypsin Inhibitor 2 at Atomic Resolution.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>98<\/i>: 4349-4354, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.071054398\">DOI<\/a>]<\/li>\n<li>Pan Y. and Daggett V. Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding.\u00a0<b>Biochemistry<\/b>\u00a0<i>40<\/i>: 2723-2731, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi0022036\">DOI<\/a>]<\/li>\n<li>Li B., Alonso D.O.V. and Daggett V. The Molecular Basis for the Inverse Temperature Transition of Elastin.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>305<\/i>: 581-592, 2001. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.2000.4306\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/11152614\">HTML<\/a>]<\/li>\n<li>Clarke J., Hounslow A.M., Bond C.J., Fersht A.R. and Daggett V. The Effect of Disulfide Bonds on the Denatured State of Barnase.\u00a0<b>Protein Science<\/b>\u00a0<i>9<\/i>: 2394-2404, 2000. [<a href=\"http:\/\/dx.doi.org\/10.1110\/ps.9.12.2394\">DOI<\/a>]<\/li>\n<li>Mayor U., Johnson C.M., Daggett V., and Fersht A.R. Protein Folding and Unfolding in Microseconds to Nanoseconds by Experiment and Simulation.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>97<\/i>: 13518-13522, 2000. [<a href=\"http:\/\/dx.doi.org\/10.1073\/pnas.250473497\">DOI<\/a>]<\/li>\n<li>Hom K., Wolfe G., Ma Q.-F., Zhang H., Storch E.M., Daggett V., Basus V.J., Waskell L. NMR Studies of the Association of Cytochrome\u00a0<i>b<\/i><sub>5<\/sub>\u00a0with Cytochrome\u00a0<i>c<\/i>:\u00a0<b>Biochemistry<\/b>\u00a0<i>39<\/i>, 14025-14039, 2000. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi001129o\">DOI<\/a>]<\/li>\n<li>Wong K., Clarke J., Bond C.J., Neira J.L., Freund S.M.V., Fersht A.R., and Daggett V. Towards Complete Characterization of the Structural and Dynamic Properties of the Denatured State of Barnase and the Role of Residual Structure in Folding.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>296<\/i>: 1257-1285, 2000. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.2000.3523\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10698632\">HTML<\/a>]<\/li>\n<li>Daggett V. and Fersht A.R. Transition States in Protein Folding.\u00a0<b>Mechanisms of Protein Folding<\/b>. Roger Pain, Editor. 2nd ed. Oxford University Press: Oxford, 175-211, 2000. [<a href=\"http:\/\/books.google.com\/books?id=DvJygJkNCYkC\">Google<\/a>]<\/li>\n<li>Alonso D.O.V. and Daggett V. Staphylococcal Protein A: Unfolding Pathways, Unfolded States, and Differences between the B and E Domains.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>97<\/i>: 133-138, 2000. [<a href=\"http:\/\/www.pnas.org\/cgi\/reprint\/97\/1\/133.pdf\">PDF<\/a>] [<a href=\"http:\/\/www.pnas.org\/cgi\/content\/abstract\/97\/1\/133\">HTML<\/a>]<\/li>\n<li>Alonso D.O.V., Alm E. and Daggett V. The Unfolding Pathway of the Cell Cycle Protein P13suc1: Implications for Domain Swapping.\u00a0<b>Structure<\/b>\u00a0<i>8<\/i>: 101-110, 2000. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0969-2126(00)00083-6\">DOI<\/a>]<\/li>\n<li>Daggett V. Molecular Dynamics Simulations of Protein Folding.\u00a0<b>Protein Structure, Stability, and Folding<\/b>. Kenneth Murphy, Editor. Humana Press: New Jersey,\u00a0<i>168<\/i>: 215-247, 2000. [<a href=\"http:\/\/books.google.com\/books?id=q3365917C4IC\">Google<\/a>]<\/li>\n<li>Daggett V. Long Timescale Simulations.\u00a0<b>Current Opinion in Structural Biology<\/b>\u00a0<i>10<\/i>: 160-164, 2000. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0959-440X(00)00062-2\">DOI<\/a>]<\/li>\n<li>DeArmond S., Qiu Y., Sanchez H., Spilman P.R., Ninchak-Casey A., Alonso, D.O.V., and Daggett V. PrP<sup>C<\/sup>\u00a0Glycoform Heterogeneity as a Function of Brain Region: Implications for Selective Targeting of Neurons by Prion Strains.\u00a0<b>Journal of Neuropathology &amp; Experimental Neurology<\/b>\u00a0<i>58<\/i>: 1000-1009, 1999. [<a href=\"http:\/\/www.jneuropath.com\/pt\/re\/jnen\/abstract.00005072-199909000-00010.htm\">HTML<\/a>] [<a href=\"http:\/\/www.jneuropath.com\/pt\/re\/jnen\/pdfhandler.00005072-199909000-00010.pdf\">PDF<\/a>]<\/li>\n<li>Fulton K.F., Main E.R.G., Daggett V., and Jackson S.E. Mapping the Interactions Present in the Transition State for Folding\/Unfolding of FKBP12.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>291<\/i>: 445-461, 1999. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1999.2942\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10438631\">HTML<\/a>]<\/li>\n<li>Kazmirski S., Li A., and Daggett V. Analysis Methods for Comparison of Molecular Dynamics Trajectories: Applications to Protein Unfolding Pathways and Denatured Ensembles.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>290<\/i>: 283-304, 1999. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1999.2843\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10388573\">HTML<\/a>]<\/li>\n<li>Storch E.M., Daggett V., and Atkins W.M. Engineering Out Motion: Introduction of a\u00a0<i>de novo<\/i>\u00a0Disulfide Bond and a Salt Bridge Designed to Close a Dynamic Cleft on the Surface of Cytochrome\u00a0<i>b<\/i><sub>5<\/sub>.\u00a0<b>Biochemistry<\/b>\u00a0<i>38<\/i>: 5054-5064, 1999. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi982158q\">DOI<\/a>]<\/li>\n<li>Storch E.M., Grinstead J.S., Campbell A.P., Daggett V., and Atkins W.M. Engineering Out Motion: A Surface Disulfide Bond Alters the Mobility of Trp 22 in Cytochrome\u00a0<i>b<\/i><sub>5<\/sub>\u00a0as Probed by Time-Resolved Fluorescence and\u00a0<sup>1<\/sup>H-NMR Experiments.\u00a0<b>Biochemistry<\/b>\u00a0<i>38<\/i>: 5065-5075, 1999. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi982159i\">DOI<\/a>]<\/li>\n<li>Ladurner A.G., Itzhaki L.S., Daggett V., and Fersht A.R. Synergy Between Simulation and Experiment in Describing the Energy Landscape of Protein Folding.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>95<\/i>: 8473-8478, 1998. [\u00a0<a href=\"http:\/\/www.pnas.org\/cgi\/reprint\/95\/15\/8473.pdf\">PDF<\/a>] [<a href=\"http:\/\/www.pnas.org\/cgi\/content\/abstract\/95\/15\/8473\">HTML<\/a>]<\/li>\n<li>Daggett V. Structure-Function Aspects of Prion Proteins.\u00a0<b>Current Opinion in Biotechnology<\/b>\u00a0<i>9<\/i>: 359-365, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0958-1669(98)80008-6\">DOI<\/a>]<\/li>\n<li>Daggett V., Li A., and Fersht A.R. A Combined Molecular Dynamics and \u03a6-Value Analysis of Structure-Reactivity Relationships in the Transition State and Unfolding Pathway of Barnase: The Structural Basis of Hammond and Anti-Hammond Effects.\u00a0<b>Journal of the American Chemical Society<\/b>\u00a0<i>120<\/i>: 12740-12754, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ja981558y\">DOI<\/a>]<\/li>\n<li>Li A. and Daggett V. Molecular Dynamics Simulation of the Unfolding of Barnase: Characterization of the Major Intermediate.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>275<\/i>: 677-694, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1997.1484\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/9466940\">HTML<\/a>]<\/li>\n<li>Li Z., Laidig K.E., and Daggett V. Conformational Search Using a Molecular Dynamics-Minimization Procedure: Applications to Clusters of Coulombic Charges, Lennard-Jones Particles and Water.\u00a0<b>Journal of Computational Chemistry<\/b>\u00a0<i>19<\/i>: 60-70, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1002\/(SICI)1096-987X(19980115)19:1%3C60::AID-JCC5%3E3.0.CO;2-X\">DOI<\/a>]<\/li>\n<li>Alonso D.O.V. and Daggett V. Molecular Dynamics Simulations of Hydrophobic Collapse of Ubiquitin.\u00a0<b>Protein Science<\/b>,\u00a0<i>7<\/i>: 860-874, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1002\/pro.5560070404\">DOI<\/a>] [<a href=\"http:\/\/www3.interscience.wiley.com\/journal\/121600856\/abstract\">HTML<\/a>]<\/li>\n<li>Kazmirski S.L. and Daggett V. Simulation of the Structural and Dynamic Properties of Unfolded Proteins: The \u201cMolten Coil\u201d State of Bovine Pancreatic Trypsin Inhibitor.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>277<\/i>: 487-506, 1998. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1998.1634\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/9514766\">HTML<\/a>]<\/li>\n<li>Wong K.B. and Daggett V. Barstar Has A Highly Dynamic Hydrophobic Core: Evidence From Molecular Dynamics Simulation And NMR Relaxation Data.\u00a0<b>Biochemistry<\/b>\u00a0<i>37<\/i>: 11182-11192, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi980552i\">DOI<\/a>]<\/li>\n<li>Laidig K.E., Gainer J.L., and Daggett V. Altering Diffusivity in Biological Solutions Through Modification of Solution Structure and Dynamics.\u00a0<b>Journal of the American Chemical Society<\/b>\u00a0<i>120<\/i>: 9394-9395, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1021\/ja981656j\">DOI<\/a>]<\/li>\n<li>Kazmirski S. and Daggett V. Non-Native Interactions in Protein Folding Intermediates: Molecular Dynamics Simulation of Hen Lysozyme.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>284<\/i>: 793-806, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1998.2192\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/9826516\">HTML<\/a>]<\/li>\n<li>Laidig K.E. and Daggett V. Protein Modeling: Folding \u2194 Unfolding Dynamics.\u00a0<i>Simulations of Biological Systems<\/i>.\u00a0<b>Encyclopedia of Computational Chemistry<\/b>. P.V.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H.F. Schaefer III, P.R. Schreiner, Editors. John Wiley &amp; Sons Ltd.: Chichester,\u00a0<i>3<\/i>: 2211-2220, 1998. [<a href=\"http:\/\/dx.doi.org\/10.1002\/0470845015.cpa032\">DOI<\/a>]<\/li>\n<li>Harrison P.M., Bamborough P., Daggett V., Prusiner S.B., and Cohen F.E. The Prion Folding Problem.\u00a0<b>Current Opinion in Structural Biology<\/b>\u00a0<i>7<\/i>: 53-59, 1997. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0959-440X(97)80007-3\">DOI<\/a>]<\/li>\n<li>Levitt M., Hirshberg M., Sharon R., Laidig K.E., and Daggett V. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution.\u00a0<b>Journal of Physical Chemistry<\/b>\u00a0<i>101<\/i>: 5051-5061, 1997. [<a href=\"http:\/\/dx.doi.org\/10.1021\/jp964020s\">DOI<\/a>]<\/li>\n<li>Kazmirski S.L. and Daggett V. Protein Dynamics: A Theoretical Perspective.\u00a0<b>Advances in Molecular and Cellular Biology<\/b>. N.M. Allewell and C.K. Woodward, Editors. JAI Press, Inc.: Greenwich,\u00a0<i>22B<\/i>: 339-390, 1997.<\/li>\n<li>Bond C.J., Wong K., Clarke J., Fersht A.R., and Daggett V. Characterization of Residual Structure in the Thermally Denatured State of Barnase by Simulation and Experiment: Description of the Folding Pathway.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>94<\/i>: 13409-13413, 1997. [<a href=\"http:\/\/www.pnas.org\/cgi\/reprint\/94\/25\/13409.pdf\">PDF<\/a>] [<a href=\"http:\/\/www.pnas.org\/cgi\/content\/abstract\/94\/25\/13409\">HTML<\/a>]<\/li>\n<li>DeArmond S., Sanchez H., Yehiely F., Qiu Y., Ninchak-Casey A., Daggett V., Paminano-Camerino A.N., Cayetano J., Rogers M., Groth D., Torchia M., Tremblay P., Scott M.R., Cohen F.E., and Prusiner S. Selective Neuronal Targeting in Prion Disease.\u00a0<b>Neuron<\/b>\u00a0<i>19<\/i>: 1337-1348, 1997. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0896-6273(00)80424-9\">DOI<\/a>]<\/li>\n<li>Storch E.A. and Daggett V. Structural Consequences of Heme Removal: Molecular Dynamics Simulations of Rat and Bovine Apocytochrome\u00a0<i>b<sub>5<\/sub><\/i>.\u00a0<b>Biochemistry<\/b>\u00a0<i>35<\/i>: 11596-11604, 1996. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi960598g\">DOI<\/a>]<\/li>\n<li>Laidig K.E. and Daggett V. Molecular Dynamics Simulations of Apocytochrome b<sub>562<\/sub>\u00a0\u2013 The Highly Ordered Limit of Molten Globules.\u00a0<b>Folding &amp; Design<\/b>\u00a0<i>1<\/i>: 335-346, 1996. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S1359-0278(96)00049-1\">DOI<\/a>]<\/li>\n<li>Kazmirski S., Alonso D.O.V., Cohen R.E., Prusiner S., and Daggett V. The Conformational Consequences of Mutations to the H1 Helix of the Prion Protein.\u00a0<b>Techniques in Protein Chemistry VII<\/b>. Daniel Marshak, Editor. Academic Press: Baltimore, 1996. [<a href=\"http:\/\/books.google.com\/books?id=nmOXAwAACAAJ\">Google<\/a>]<\/li>\n<li>Daggett V., Li A., Itzhaki L.S., Otzen D.E., and Fersht A.R. Structure of the Transition State for Folding of a Protein Derived from Experiment and Simulation.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>257<\/i>: 430-440, 1996. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1996.0173\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/8609634\">HTML<\/a>]<\/li>\n<li>Li A. and Daggett V. Indentification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics Simulations.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>257<\/i>: 412-429, 1996. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1996.0172\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/8609633\">HTML<\/a>]<\/li>\n<li>Laidig K.E. and Daggett V. Testing the Modified Hydration-Shell Hydrogen-Bond Model of Hydrophobic Effects using Molecular Dynamics Simulation.\u00a0<b>Journal of Physical Chemistry<\/b>\u00a0<i>100<\/i>: 5616-5619, 1996. [<a href=\"http:\/\/dx.doi.org\/10.1021\/jp960520+\">DOI<\/a>]<\/li>\n<li>Li A. and Daggett V. Investigation of the Solution Structure of Chymotrypsin Inhibitor 2 using Molecular Dynamics: Comparison to X-ray Crystallographic and NMR Data.\u00a0<b>Protein Engineering<\/b>\u00a0<i>8<\/i>: 1117-1128, 1995. [<a href=\"http:\/\/peds.oxfordjournals.org\/cgi\/reprint\/8\/11\/1117.pdf\">PDF<\/a>] [<a href=\"http:\/\/peds.oxfordjournals.org\/cgi\/content\/abstract\/8\/11\/1117\">HTML<\/a>]<\/li>\n<li>Alonso D.O.V. and V. Daggett V. Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding: Characterization of Partially Unfolded States of Ubiquitin in 60% Methanol and in Water.\u00a0<b>Journal of Molecular Biology<\/b>\u00a0<i>247<\/i>: 501-520, 1995. [<a href=\"http:\/\/dx.doi.org\/10.1006\/jmbi.1994.0156\">DOI<\/a>] [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/7714903\">HTML<\/a>]<\/li>\n<li>Kazmirski S., Alonso D.O.V, Cohen F.E., Prusiner S., and Daggett V. Theoretical Studies of Sequence Effects on the Conformational Properties of a Fragment of the Prion Protein: Implications for Scrapie Formation.\u00a0<b>Chemistry &amp; Biology<\/b>\u00a0<i>2<\/i>: 305-315, 1995. [<a href=\"http:\/\/dx.doi.org\/10.1016\/1074-5521(95)90049-7\">DOI<\/a>]<\/li>\n<li>Storch E.M. and Daggett V., Molecular Dynamics Simulations of Cytochrome\u00a0<i>b<\/i><sub>5<\/sub>: Implications for Protein\u2013Protein Recognition.\u00a0<b>Biochemistry<\/b>\u00a0<i>34<\/i>: 9682-9693, 1995. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi00030a005\">DOI<\/a>]<\/li>\n<li>Kirshenbaum K. and Daggett V. pH-Dependent Conformations of the Amyloid \u03b2(1-28) Peptide Fragment Explored Using Molecular Dynamics.\u00a0<b>Biochemistry<\/b>\u00a0<i>34<\/i>: 7629-7639, 1995. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi00023a009\">DOI<\/a>]<\/li>\n<li>Kirshenbaum K. and Daggett V. Sequence Effects on the Conformational Properties of the Amyloid \u03b2(1-28) Peptide: Testing a Proposed Mechanism for the \u03b1 \u2192 \u03b2 Transition.\u00a0<b>Biochemistry<\/b>\u00a0<i>34<\/i>: 7640-7647, 1995. [<a href=\"http:\/\/dx.doi.org\/10.1021\/bi00023a010\">DOI<\/a>]<\/li>\n<li>Levitt M., Hirshberg M., Sharon R., and Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution.\u00a0<b>Computer Physics Communications<\/b>\u00a0<i>91<\/i>: 215-231, 1995. [\u00a0<a href=\"http:\/\/dx.doi.org\/10.1016\/0010-4655(95)00049-L\">DOI<\/a>]<\/li>\n<li>Li A. and Daggett V. Characterization of the Transition State of Protein Unfolding Using Molecular Dynamics: Chymotrypsin Inhibitor 2.\u00a0<b>Proceedings of the National Academy of Sciences USA<\/b>\u00a0<i>91<\/i>: 10430-10434, 1994. [<a href=\"http:\/\/www.pnas.org\/cgi\/reprint\/91\/22\/10430.pdf\">PDF<\/a>] [<a href=\"http:\/\/www.pnas.org\/cgi\/content\/abstract\/91\/22\/10430\">HTML<\/a>]<\/li>\n<li>Daggett V. and Levitt M. Protein Folding\u2192Unfolding Dynamics.\u00a0<b>Current Opinion in Structural Biology<\/b>\u00a0<i>4<\/i>: 291-295, 1994. [<a href=\"http:\/\/dx.doi.org\/10.1016\/S0959-440X(94)90322-0\">DOI<\/a>]<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Publications<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-196","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/pages\/196","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/comments?post=196"}],"version-history":[{"count":3,"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/pages\/196\/revisions"}],"predecessor-version":[{"id":2147,"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/pages\/196\/revisions\/2147"}],"wp:attachment":[{"href":"https:\/\/sites.bioe.uw.edu\/daggett\/wp-json\/wp\/v2\/media?parent=196"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}