| Year |
Citation |
Score |
| 2023 |
Bleem A, Prosswimmer T, Chen R, Hady TF, Li J, Bryers JD, Daggett V. Designed α-sheet peptides disrupt uropathogenic E. coli biofilms rendering bacteria susceptible to antibiotics and immune cells. Scientific Reports. 13: 9272. PMID 37286572 DOI: 10.1038/s41598-023-36343-6 |
0.759 |
|
| 2022 |
Childers MC, Daggett V. Molecular Dynamics Methods for Antibody Design. Methods in Molecular Biology (Clifton, N.J.). 2552: 109-124. PMID 36346588 DOI: 10.1007/978-1-0716-2609-2_5 |
0.714 |
|
| 2020 |
Childers MC, Geeves M, Daggett V, Regnier M. Modulation of post-powerstroke dynamics in myosin II by 2'-deoxy-ADP. Archives of Biochemistry and Biophysics. 699: 108733. PMID 33388313 DOI: 10.1016/j.abb.2020.108733 |
0.714 |
|
| 2020 |
Demakis C, Childers MC, Daggett V. Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues. Protein Science : a Publication of the Protein Society. PMID 33190305 DOI: 10.1002/pro.3998 |
0.729 |
|
| 2020 |
Childers MC, Daggett V. Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions. Biophysical Journal. 119: 1995-2009. PMID 33091379 DOI: 10.1016/j.bpj.2020.08.043 |
0.769 |
|
| 2020 |
Ma W, Childers M, Murray J, Moussavi-Harami F, Gong H, Weiss R, Daggett V, Irving T, Regnier M. Myosin dynamics during relaxation in mouse soleus muscle and modulation by 2'-deoxy-ATP. The Journal of Physiology. PMID 32818298 DOI: 10.1113/Jp280402 |
0.724 |
|
| 2020 |
Bromley D, Daggett V. Tumorigenic p53 Mutants Undergo Common Structural Disruptions Including Conversion to α‐Sheet Structure Protein Science. 29: 1983-1999. PMID 32715544 DOI: 10.1002/Pro.3921 |
0.81 |
|
| 2020 |
Childers MC, Daggett V, Regnier M. Nucleotide-Dependent Allosteric Communication in Myosin Biophysical Journal. 118: 425a. DOI: 10.1016/J.Bpj.2019.11.2393 |
0.672 |
|
| 2020 |
Childers MC, Daggett V, Regnier M. Cross-Species Dynamics of Myosin in Pre-Powerstroke States Biophysical Journal. 118: 422a. DOI: 10.1016/J.Bpj.2019.11.2380 |
0.711 |
|
| 2019 |
Toofanny RD, Calhoun S, Jonsson AL, Daggett V. Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins. Protein Engineering, Design & Selection : Peds. PMID 31868211 DOI: 10.1093/Protein/Gzz040 |
0.833 |
|
| 2019 |
Childers MC, Daggett V. Drivers of α-Sheet Formation in Transthyretin under Amyloidogenic Conditions. Biochemistry. 58: 4408-4423. PMID 31609590 DOI: 10.1021/Acs.Biochem.9B00769 |
0.775 |
|
| 2019 |
Powers JD, Yuan CC, McCabe KJ, Murray JD, Childers MC, Flint GV, Moussavi-Harami F, Mohran S, Castillo R, Zuzek C, Ma W, Daggett V, McCulloch AD, Irving TC, Regnier M. Cardiac myosin activation with 2-deoxy-ATP via increased electrostatic interactions with actin. Proceedings of the National Academy of Sciences of the United States of America. PMID 31110001 DOI: 10.1073/Pnas.1905028116 |
0.731 |
|
| 2019 |
Shea D, Hsu CC, Bi TM, Paranjapye N, Childers MC, Cochran J, Tomberlin CP, Wang L, Paris D, Zonderman J, Varani G, Link CD, Mullan M, Daggett V. α-Sheet secondary structure in amyloid β-peptide drives aggregation and toxicity in Alzheimer's disease. Proceedings of the National Academy of Sciences of the United States of America. PMID 31004062 DOI: 10.1073/Pnas.1820585116 |
0.713 |
|
| 2019 |
Ferina J, Daggett V. Visualizing Protein Folding and Unfolding. Journal of Molecular Biology. 431: 1540-1564. PMID 30840846 DOI: 10.1016/J.Jmb.2019.02.026 |
0.483 |
|
| 2019 |
Ma W, Childers MC, Murray JD, Gong H, Daggett V, Irving TC, Regnier M. Time-Resolved X-Ray Diffraction and Molecular Dynamics Studies of Skeletal Muscle Relaxation with 2 Deoxy-ATP Biophysical Journal. 116: 403a-404a. DOI: 10.1016/J.Bpj.2018.11.2180 |
0.696 |
|
| 2019 |
Childers MC, Ma W, Daggett V, Regnier M. Molecular Dynamics Studies of Myosin Structure with 2-Deoxy-ADP Biophysical Journal. 116: 265a. DOI: 10.1016/J.Bpj.2018.11.1437 |
0.748 |
|
| 2018 |
Gianni S, McCully M, Malagrinò F, Bonetti D, De Simone A, Brunori M, Daggett V. A carboxylate to amide substitution tunes fold switching in a protein domain. Angewandte Chemie (International Ed. in English). PMID 30098087 DOI: 10.1002/Anie.201807723 |
0.689 |
|
| 2018 |
Paranjapye N, Daggett V. De Novo Designed Alpha-Sheet Peptides Inhibit Functional Amyloid Formation of Streptococcus Mutans Biofilms. Journal of Molecular Biology. PMID 30006266 DOI: 10.1016/J.Jmb.2018.07.005 |
0.326 |
|
| 2018 |
Childers MC, Towse CL, Daggett V. Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides. Protein Engineering, Design & Selection : Peds. PMID 29992252 DOI: 10.1093/Protein/Gzy016 |
0.744 |
|
| 2018 |
Bleem A, Christiansen G, Madsen DJ, Maric H, Strømgaard K, Bryers JD, Daggett V, Meyer RL, Otzen DE. Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms. Journal of Molecular Biology. PMID 29964047 DOI: 10.1016/J.Jmb.2018.06.043 |
0.789 |
|
| 2018 |
Childers M, Daggett V. Validating Molecular Dynamics Simulations Against Experimental Observables in Light of Underlying Conformational Ensembles. The Journal of Physical Chemistry. B. PMID 29864281 DOI: 10.1021/Acs.Jpcb.8B02144 |
0.785 |
|
| 2018 |
Childers MC, Daggett V. Drivers of Conformational Variability in Transthyretin Monomers under Amyloidogenic Conditions Biophysical Journal. 114: 234a. DOI: 10.1016/J.Bpj.2017.11.1304 |
0.708 |
|
| 2017 |
Maris NL, Shea D, Bleem A, Bryers JD, Daggett V. Chemical and Physical Variability in Structural Isomers of an l/d α-Sheet Peptide Designed To Inhibit Amyloidogenesis. Biochemistry. PMID 29202245 DOI: 10.1021/Acs.Biochem.7B00345 |
0.782 |
|
| 2017 |
Bleem A, Francisco R, Bryers JD, Daggett V. Designed α-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilms. Npj Biofilms and Microbiomes. 3: 16. PMID 28685098 DOI: 10.1038/s41522-017-0025-2 |
0.773 |
|
| 2017 |
Cheng CJ, Koldsø H, Van der Kamp MW, Schiøtt B, Daggett V. Simulations of Membrane-bound Diglycosylated Human Prion Protein Reveal Potential Protective Mechanisms against Misfolding. Journal of Neurochemistry. PMID 28407243 DOI: 10.1111/Jnc.14044 |
0.705 |
|
| 2017 |
Towse CL, Akke M, Daggett V. The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy Across Protein Fold Space. The Journal of Physical Chemistry. B. PMID 28375008 DOI: 10.1021/Acs.Jpcb.7B00577 |
0.479 |
|
| 2017 |
Childers MC, Daggett V. Insights from molecular dynamics simulations for computational protein design. Molecular Systems Design & Engineering. 2: 9-33. PMID 28239489 DOI: 10.1039/C6ME00083E |
0.786 |
|
| 2017 |
Nowakowski SG, Regnier M, Daggett V. Molecular mechanisms underlying deoxy-ADP.Pi activation of pre-powerstroke myosin. Protein Science : a Publication of the Protein Society. PMID 28097776 DOI: 10.1002/Pro.3121 |
0.327 |
|
| 2016 |
Bromley D, Bauer MR, Fersht AR, Daggett V. An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein. Protein Engineering, Design & Selection : Peds. PMID 27503952 DOI: 10.1093/Protein/Gzw035 |
0.791 |
|
| 2016 |
Bleem A, Daggett V. Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering. Biotechnology and Bioengineering. PMID 27474784 DOI: 10.1002/Bit.26059 |
0.794 |
|
| 2016 |
Childers MC, Towse CL, Daggett V. The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design. Protein Engineering, Design & Selection : Peds. PMID 27284086 DOI: 10.1093/Protein/Gzw023 |
0.746 |
|
| 2016 |
Kellock J, Hopping G, Caughey B, Daggett V. Peptides comprised of alternating L- and D- Amino acids inhibit amyloidogenesis in Three Distinct Amyloid Systems independent of sequence. Journal of Molecular Biology. PMID 27012425 DOI: 10.1016/J.Jmb.2016.03.013 |
0.59 |
|
| 2016 |
Towse CL, Vymetal J, Vondrasek J, Daggett V. Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series. Biophysical Journal. 110: 348-61. PMID 26789758 DOI: 10.1016/J.Bpj.2015.12.008 |
0.468 |
|
| 2016 |
Towse CL, Rysavy SJ, Vulovic IM, Daggett V. New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. Structure (London, England : 1993). 24: 187-99. PMID 26745530 DOI: 10.1016/J.Str.2015.10.017 |
0.492 |
|
| 2014 |
Towse CL, Hopping G, Vulovic I, Daggett V. Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality. Protein Engineering, Design & Selection : Peds. 27: 447-55. PMID 25233851 DOI: 10.1093/Protein/Gzu037 |
0.322 |
|
| 2014 |
Rysavy SJ, Beck DA, Daggett V. Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction. Protein Science : a Publication of the Protein Society. 23: 1584-95. PMID 25142412 DOI: 10.1002/Pro.2537 |
0.456 |
|
| 2014 |
Hopping G, Kellock J, Barnwal RP, Law P, Bryers J, Varani G, Caughey B, Daggett V. Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers. Elife. 3: e01681. PMID 25027691 DOI: 10.7554/Elife.01681 |
0.61 |
|
| 2014 |
Rysavy SJ, Bromley D, Daggett V. DIVE: a graph-based visual-analytics framework for big data. Ieee Computer Graphics and Applications. 34: 26-37. PMID 24808197 DOI: 10.1109/Mcg.2014.27 |
0.776 |
|
| 2014 |
Merkley ED, Rysavy S, Kahraman A, Hafen RP, Daggett V, Adkins JN. Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Science : a Publication of the Protein Society. 23: 747-59. PMID 24639379 DOI: 10.1002/Pro.2458 |
0.744 |
|
| 2014 |
Chen W, van der Kamp MW, Daggett V. Structural and dynamic properties of the human prion protein. Biophysical Journal. 106: 1152-63. PMID 24606939 DOI: 10.1016/J.Bpj.2013.12.053 |
0.735 |
|
| 2014 |
Cheng CJ, Daggett V. Different misfolding mechanisms converge on common conformational changes: human prion protein pathogenic mutants Y218N and E196K. Prion. 8: 125-35. PMID 24509603 DOI: 10.4161/Pri.27807 |
0.414 |
|
| 2014 |
Bromley D, Rysavy SJ, Su R, Toofanny RD, Schmidlin T, Daggett V. DIVE: a data intensive visualization engine. Bioinformatics (Oxford, England). 30: 593-5. PMID 24336804 DOI: 10.1093/Bioinformatics/Btt721 |
0.773 |
|
| 2013 |
Hopping G, Kellock J, Caughey B, Daggett V. Designed Trpzip-3 β-Hairpin Inhibits Amyloid Formation in Two Different Amyloid Systems. Acs Medicinal Chemistry Letters. 4: 824-8. PMID 24900756 DOI: 10.1021/Ml300478W |
0.575 |
|
| 2013 |
Bromley D, Daggett V. Analyzing disease-associated protein structures with visual analytics. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2013: 33. PMID 24303293 |
0.821 |
|
| 2013 |
Schmidlin T, Ploeger K, Jonsson AL, Daggett V. Early steps in thermal unfolding of superoxide dismutase 1 are similar to the conformational changes associated with the ALS-associated A4V mutation. Protein Engineering, Design & Selection : Peds. 26: 503-13. PMID 23784844 DOI: 10.1093/Protein/Gzt030 |
0.451 |
|
| 2013 |
Bromley D, Anderson PC, Daggett V. Structural consequences of mutations to the α-tocopherol transfer protein associated with the neurodegenerative disease ataxia with vitamin E deficiency. Biochemistry. 52: 4264-73. PMID 23713716 DOI: 10.1021/Bi4001084 |
0.801 |
|
| 2013 |
Wang D, McCully ME, Luo Z, McMichael J, Tu AY, Daggett V, Regnier M. Structural and functional consequences of cardiac troponin C L57Q and I61Q Ca(2+)-desensitizing variants. Archives of Biochemistry and Biophysics. 535: 68-75. PMID 23454346 DOI: 10.1016/J.Abb.2013.02.006 |
0.597 |
|
| 2013 |
Rizzuti B, Daggett V. Using simulations to provide the framework for experimental protein folding studies. Archives of Biochemistry and Biophysics. 531: 128-35. PMID 23266569 DOI: 10.1016/J.Abb.2012.12.015 |
0.518 |
|
| 2013 |
McCully ME, Beck DA, Daggett V. Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. Protein Engineering, Design & Selection : Peds. 26: 35-45. PMID 23012442 DOI: 10.1016/J.Bpj.2016.11.354 |
0.706 |
|
| 2013 |
Nowakowski SG, Adamek N, Geeves MA, Gay E, Kolwicz SC, Murry CE, Daggett V, Regnier M. 2-deoxy-ATP Alters Myosin Structure to Enhance Cross-Bridge Cycling and Improve Cardiac Function Biophysical Journal. 104: 17a. DOI: 10.1016/J.Bpj.2012.11.125 |
0.331 |
|
| 2012 |
Benson NC, Daggett V. Wavelet Analysis of Protein Motion. International Journal of Wavelets, Multiresolution and Information Processing. 10. PMID 25484480 DOI: 10.1142/S0219691312500403 |
0.457 |
|
| 2012 |
Simms AM, Daggett V. Protein Simulation Data in the Relational Model. The Journal of Supercomputing. 62: 150-173. PMID 23204646 DOI: 10.1007/S11227-011-0692-3 |
0.809 |
|
| 2012 |
Towse CL, Daggett V. When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 34: 1060-9. PMID 23108912 DOI: 10.1002/Bies.201200116 |
0.372 |
|
| 2012 |
McCully ME, Beck DA, Daggett V. Multimolecule test-tube simulations of protein unfolding and aggregation. Proceedings of the National Academy of Sciences of the United States of America. 109: 17851-6. PMID 23091038 DOI: 10.1073/Pnas.1201809109 |
0.724 |
|
| 2012 |
Benson NC, Daggett V. A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations. Journal of Bioinformatics and Computational Biology. 10: 1250008. PMID 22809421 DOI: 10.1142/S0219720012500084 |
0.335 |
|
| 2012 |
Wang D, Robertson IM, Li MX, McCully ME, Crane ML, Luo Z, Tu AY, Daggett V, Sykes BD, Regnier M. Structural and functional consequences of the cardiac troponin C L48Q Ca(2+)-sensitizing mutation. Biochemistry. 51: 4473-87. PMID 22591429 DOI: 10.1021/Bi3003007 |
0.6 |
|
| 2012 |
Benson NC, Daggett V. A comparison of multiscale methods for the analysis of molecular dynamics simulations. The Journal of Physical Chemistry. B. 116: 8722-31. PMID 22494262 DOI: 10.1021/Jp302103T |
0.494 |
|
| 2012 |
Scouras AD, Daggett V. Disruption of the X-loop turn of the prion protein linked to scrapie resistance. Protein Engineering, Design & Selection : Peds. 25: 243-9. PMID 22447804 DOI: 10.1093/Protein/Gzs009 |
0.809 |
|
| 2012 |
Merkley ED, Daggett V, Parson WW. A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8. Proteins. 80: 546-55. PMID 22081476 DOI: 10.1002/Prot.23219 |
0.773 |
|
| 2012 |
Jonsson AL, Fersht AR, Daggett V. Combining simulation and experiment to map protein folding Comprehensive Biophysics. 3: 1-18. DOI: 10.1016/B978-0-12-374920-8.00301-5 |
0.503 |
|
| 2012 |
Toofanny RD, Daggett V. Understanding protein unfolding from molecular simulations Wiley Interdisciplinary Reviews: Computational Molecular Science. 2: 405-423. DOI: 10.1002/Wcms.1088 |
0.835 |
|
| 2011 |
Morrone A, Giri R, Toofanny RD, Travaglini-Allocatelli C, Brunori M, Daggett V, Gianni S. GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate. Biophysical Journal. 101: 2053-60. PMID 22004760 DOI: 10.1016/J.Bpj.2011.09.013 |
0.822 |
|
| 2011 |
Jonsson AL, Daggett V. The effect of context on the folding of β-hairpins. Journal of Structural Biology. 176: 143-50. PMID 21843644 DOI: 10.1016/J.Jsb.2011.08.001 |
0.429 |
|
| 2011 |
Toofanny RD, Simms AM, Beck DA, Daggett V. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. Bmc Bioinformatics. 12: 334. PMID 21831299 DOI: 10.1186/1471-2105-12-334 |
0.795 |
|
| 2011 |
Calhoun S, Daggett V. Structural effects of the L145Q, V157F, and R282W cancer-associated mutations in the p53 DNA-binding core domain. Biochemistry. 50: 5345-53. PMID 21561095 DOI: 10.1021/Bi200192J |
0.372 |
|
| 2011 |
van der Kamp MW, Daggett V. Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations. Topics in Current Chemistry. 305: 169-97. PMID 21526434 DOI: 10.1007/128_2011_158 |
0.724 |
|
| 2011 |
Banachewicz W, Religa TL, Schaeffer RD, Daggett V, Fersht AR. Malleability of folding intermediates in the homeodomain superfamily Proceedings of the National Academy of Sciences of the United States of America. 108: 5596-5601. PMID 21422286 DOI: 10.1073/Pnas.1101752108 |
0.607 |
|
| 2011 |
Scouras AD, Daggett V. The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Protein Science : a Publication of the Protein Society. 20: 341-52. PMID 21280126 DOI: 10.1002/Pro.565 |
0.829 |
|
| 2011 |
Dar TA, Schaeffer RD, Daggett V, Bowler BE. Manifestations of native topology in the denatured state ensemble of Rhodopseudomonas palustris cytochrome c'. Biochemistry. 50: 1029-41. PMID 21190388 DOI: 10.1021/Bi101551H |
0.382 |
|
| 2011 |
Daggett V. Introduction to special issue 'Three decades of protein engineering: impact on structural biology and therapy'. Protein Engineering, Design & Selection : Peds. 24: 1. PMID 21149387 DOI: 10.1093/Protein/Gzq117 |
0.342 |
|
| 2011 |
Morrone A, McCully ME, Bryan PN, 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. The Journal of Biological Chemistry. 286: 3863-72. PMID 21118804 DOI: 10.1074/Jbc.M110.155911 |
0.684 |
|
| 2011 |
Schaeffer RD, Jonsson AL, Simms AM, Daggett V. Generation of a consensus protein domain dictionary. Bioinformatics (Oxford, England). 27: 46-54. PMID 21068000 DOI: 10.1093/Bioinformatics/Btq625 |
0.82 |
|
| 2011 |
Schaeffer RD, Daggett V. Protein folds and protein folding. Protein Engineering, Design & Selection : Peds. 24: 11-9. PMID 21051320 DOI: 10.1093/Protein/Gzq096 |
0.481 |
|
| 2011 |
Wang D, Korte FS, McMichael J, Luo CZ, Tu A, McCully ME, Daggett V, Regnier M. Mutations that Alter cTnC Ca2+ Binding Affect Interactions with cTnI and Cardiomyocyte Contraction Biophysical Journal. 100: 360a. DOI: 10.1016/J.Bpj.2010.12.2159 |
0.58 |
|
| 2010 |
Jonsson AL, Schaeffer RD, van der Kamp MW, Daggett V. Dynameomics: protein dynamics and unfolding across fold space. Biomolecular Concepts. 1: 335-44. PMID 25962007 DOI: 10.1515/Bmc.2010.032 |
0.743 |
|
| 2010 |
Chen W, van der Kamp MW, Daggett V. Diverse effects on the native β-sheet of the human prion protein due to disease-associated mutations. Biochemistry. 49: 9874-81. PMID 20949975 DOI: 10.1021/Bi101449F |
0.653 |
|
| 2010 |
van der Kamp MW, Daggett V. Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding. Journal of Molecular Biology. 404: 732-48. PMID 20932979 DOI: 10.1016/J.Jmb.2010.09.060 |
0.692 |
|
| 2010 |
van der Kamp MW, Daggett V. Influence of pH on the human prion protein: insights into the early steps of misfolding. Biophysical Journal. 99: 2289-98. PMID 20923664 DOI: 10.1016/J.Bpj.2010.07.063 |
0.675 |
|
| 2010 |
McCully ME, Beck DAC, Fersht AR, Daggett V. Refolding the engrailed homeodomain: Structural basis for the accumulation of a folding intermediate Biophysical Journal. 99: 1628-1636. PMID 20816076 DOI: 10.1016/J.Bpj.2010.06.040 |
0.771 |
|
| 2010 |
Toofanny RD, Jonsson AL, Daggett V. A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding. Biophysical Journal. 98: 2671-81. PMID 20513412 DOI: 10.1016/J.Bpj.2010.02.048 |
0.841 |
|
| 2010 |
van der Kamp MW, Schaeffer RD, Jonsson AL, Scouras AD, Simms AM, Toofanny RD, Benson NC, Anderson PC, Merkley ED, Rysavy S, Bromley D, Beck DA, Daggett V. Dynameomics: a comprehensive database of protein dynamics. Structure (London, England : 1993). 18: 423-35. PMID 20399180 DOI: 10.1016/J.Str.2010.01.012 |
0.802 |
|
| 2010 |
Rutherford K, Daggett V. Polymorphisms and disease: hotspots of inactivation in methyltransferases. Trends in Biochemical Sciences. 35: 531-8. PMID 20382027 DOI: 10.1016/J.Tibs.2010.03.007 |
0.391 |
|
| 2010 |
Merkley ED, Parson WW, Daggett V. Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold. Protein Engineering, Design & Selection : Peds. 23: 327-36. PMID 20083491 DOI: 10.1093/Protein/Gzp090 |
0.801 |
|
| 2010 |
Law PB, Daggett V. The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures. Protein Engineering, Design & Selection : Peds. 23: 27-33. PMID 19917655 DOI: 10.1093/Protein/Gzp069 |
0.366 |
|
| 2010 |
Wang D, McCully ME, Luo Z, Tu A, Daggett V, Regnier M. Effects of Cardiac TnC Variants on cTnC-cTnI Interaction;Solution and Molecular Dynamics Simulation Studies Biophysical Journal. 98: 149a-150a. DOI: 10.1016/J.Bpj.2009.12.805 |
0.638 |
|
| 2010 |
Toofanny RD, Cortajarena AL, Regan L, Daggett V. Molecular Dynamics Simulations of Consensus Tetratricopeptide Repeat Proteins Biophysical Journal. 98: 636a-637a. DOI: 10.1016/J.Bpj.2009.12.3486 |
0.845 |
|
| 2010 |
Schaeffer RD, Daggett V. Identification of Multiple Folding Pathways Shared by Three-Helix Bundle Proteins Biophysical Journal. 98: 636a. DOI: 10.1016/J.Bpj.2009.12.3485 |
0.495 |
|
| 2010 |
Jonsson AL, Daggett V. Importance of Protein Context on the Unfolding Pathways of β-hairpins Biophysical Journal. 98: 636a. DOI: 10.1016/J.Bpj.2009.12.3483 |
0.443 |
|
| 2010 |
Benson NC, Daggett V. Determining the Molecular Basis of Disease in Single Nucleotide Polymorphism Variants using Wavelet Analysis Biophysical Journal. 98: 570a. DOI: 10.1016/J.Bpj.2009.12.3094 |
0.371 |
|
| 2009 |
Key J, Scheuermann TH, Anderson PC, Daggett V, Gardner KH. Principles of ligand binding within a completely buried cavity in HIF2α PAS-B Journal of the American Chemical Society. 131: 17647-17654. PMID 19950993 DOI: 10.1021/Ja9073062 |
0.359 |
|
| 2009 |
Jonsson AL, Scott KA, Daggett V. Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. Biophysical Journal. 97: 2958-66. PMID 19948125 DOI: 10.1016/J.Bpj.2009.09.012 |
0.496 |
|
| 2009 |
Rutherford K, Daggett V. The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface. Protein Engineering, Design & Selection : Peds. 22: 713-21. PMID 19801578 DOI: 10.1093/Protein/Gzp056 |
0.343 |
|
| 2009 |
Schmidlin T, Kennedy BK, Daggett V. Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V. Biophysical Journal. 97: 1709-18. PMID 19751676 DOI: 10.1016/J.Bpj.2009.06.043 |
0.456 |
|
| 2009 |
van der Kamp MW, Daggett V. The consequences of pathogenic mutations to the human prion protein. Protein Engineering, Design & Selection : Peds. 22: 461-8. PMID 19602567 DOI: 10.1093/Protein/Gzp039 |
0.654 |
|
| 2009 |
Anderson PC, Daggett V. The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/beta-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding. Journal of the American Chemical Society. 131: 9506-15. PMID 19537786 DOI: 10.1021/Ja809726E |
0.311 |
|
| 2009 |
Rutherford K, Daggett V. A hotspot of inactivation: The A22S and V108M polymorphisms individually destabilize the active site structure of catechol O-methyltransferase. Biochemistry. 48: 6450-60. PMID 19435324 DOI: 10.1021/Bi900174V |
0.355 |
|
| 2009 |
DeMarco ML, 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. Journal of Neurochemistry. 109: 60-73. PMID 19226372 DOI: 10.1111/J.1471-4159.2009.05892.X |
0.45 |
|
| 2009 |
Daggett V, Fersht AR. Protein folding and binding: moving into unchartered territory Current Opinion in Structural Biology. 19: 1-2. PMID 19217770 DOI: 10.1016/J.Sbi.2009.01.006 |
0.549 |
|
| 2008 |
Benson NC, Daggett V. Dynameomics: large-scale assessment of native protein flexibility. Protein Science : a Publication of the Protein Society. 17: 2038-50. PMID 18796694 DOI: 10.1110/Ps.037473.108 |
0.537 |
|
| 2008 |
Beck DA, Alonso DO, Inoyama D, Daggett V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proceedings of the National Academy of Sciences of the United States of America. 105: 12259-64. PMID 18713857 DOI: 10.1073/Pnas.0706527105 |
0.47 |
|
| 2008 |
Anderson PC, Daggett V. Molecular basis for the structural instability of human DJ-1 induced by the L166P mutation associated with Parkinson's disease. Biochemistry. 47: 9380-93. PMID 18707128 DOI: 10.1021/Bi800677K |
0.398 |
|
| 2008 |
McCully ME, Beck DA, Daggett V. Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain. Biochemistry. 47: 7079-89. PMID 18553935 DOI: 10.1021/Bi800118B |
0.698 |
|
| 2008 |
Rutherford K, Daggett V. Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics. Journal of Molecular Biology. 379: 803-14. PMID 18482735 DOI: 10.1016/J.Jmb.2008.04.032 |
0.408 |
|
| 2008 |
Rutherford K, Alphandéry E, McMillan A, Daggett V, Parson WW. The V108M mutation decreases the structural stability of catechol O-methyltransferase. Biochimica Et Biophysica Acta. 1784: 1098-105. PMID 18474266 DOI: 10.1016/J.Bbapap.2008.04.006 |
0.604 |
|
| 2008 |
Smolin N, Li B, Beck DA, Daggett V. Side-chain dynamics are critical for water permeation through aquaporin-1. Biophysical Journal. 95: 1089-98. PMID 18441032 DOI: 10.1529/Biophysj.107.125187 |
0.358 |
|
| 2008 |
Beck DA, Jonsson AL, Schaeffer RD, Scott KA, Day R, Toofanny RD, Alonso DO, Daggett V. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Engineering, Design & Selection : Peds. 21: 353-68. PMID 18411224 DOI: 10.1093/Protein/Gzn011 |
0.849 |
|
| 2008 |
Simms AM, Toofanny RD, Kehl C, Benson NC, Daggett V. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. Protein Engineering, Design & Selection : Peds. 21: 369-77. PMID 18411223 DOI: 10.1093/Protein/Gzn012 |
0.818 |
|
| 2008 |
Kehl C, Simms AM, Toofanny RD, Daggett V. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data. Protein Engineering, Design & Selection : Peds. 21: 379-86. PMID 18411222 DOI: 10.1093/Protein/Gzn015 |
0.811 |
|
| 2008 |
Steward RE, Armen RS, Daggett V. Different disease-causing mutations in transthyretin trigger the same conformational conversion. Protein Engineering, Design & Selection : Peds. 21: 187-95. PMID 18276611 DOI: 10.1093/Protein/Gzm086 |
0.729 |
|
| 2008 |
Schaeffer RD, Fersht A, Daggett V. Combining experiment and simulation in protein folding: closing the gap for small model systems. Current Opinion in Structural Biology. 18: 4-9. PMID 18242977 DOI: 10.1016/J.Sbi.2007.11.007 |
0.637 |
|
| 2008 |
Merkley ED, Bernard B, Daggett V. Conformational changes below the Tm: molecular dynamics studies of the thermal pretransition of ribonuclease A. Biochemistry. 47: 880-92. PMID 18161991 DOI: 10.1021/Bi701565B |
0.747 |
|
| 2008 |
Rutherford K, Parson WW, Daggett V. The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics. Biochemistry. 47: 893-901. PMID 18154359 DOI: 10.1021/Bi701737F |
0.66 |
|
| 2008 |
Scouras AD, Daggett V. Species variation in PrPSc protofibril models Journal of Materials Science. 43: 3625-3637. DOI: 10.1007/S10853-008-2578-1 |
0.803 |
|
| 2007 |
Beck DA, Daggett V. A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Biophysical Journal. 93: 3382-91. PMID 17978165 DOI: 10.1529/Biophysj.106.100149 |
0.472 |
|
| 2007 |
Beck DA, Bennion BJ, Alonso DO, 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. Methods in Enzymology. 428: 373-96. PMID 17875430 DOI: 10.1016/S0076-6879(07)28022-X |
0.752 |
|
| 2007 |
Sharpe T, Jonsson AL, Rutherford TJ, Daggett V, Fersht AR. The role of the turn in β-hairpin formation during WW domain folding Protein Science. 16: 2233-2239. PMID 17766370 DOI: 10.1110/Ps.073004907 |
0.579 |
|
| 2007 |
DeMarco ML, Daggett V. Molecular mechanism for low pH triggered misfolding of the human prion protein. Biochemistry. 46: 3045-54. PMID 17315950 DOI: 10.1021/Bi0619066 |
0.47 |
|
| 2007 |
Scott KA, Alonso DO, Sato S, Fersht AR, Daggett V. Conformational entropy of alanine versus glycine in protein denatured states. Proceedings of the National Academy of Sciences of the United States of America. 104: 2661-6. PMID 17307875 DOI: 10.1073/Pnas.0611182104 |
0.601 |
|
| 2007 |
Scott KA, Daggett V. Folding mechanisms of proteins with high sequence identity but different folds. Biochemistry. 46: 1545-56. PMID 17279619 DOI: 10.1021/Bi061904L |
0.455 |
|
| 2007 |
Day R, Daggett V. Direct observation of microscopic reversibility in single-molecule protein folding. Journal of Molecular Biology. 366: 677-86. PMID 17174331 DOI: 10.1016/J.Jmb.2006.11.043 |
0.478 |
|
| 2007 |
Beck DA, White GW, Daggett V. Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Journal of Structural Biology. 157: 514-23. PMID 17113307 DOI: 10.1016/J.Jsb.2006.10.002 |
0.489 |
|
| 2007 |
Fersht AR, Daggett V. Folding and binding: implementing the game plan Current Opinion in Structural Biology. 17: 1-2. DOI: 10.1016/J.Sbi.2007.01.011 |
0.45 |
|
| 2006 |
DeMarco ML, Silveira J, Caughey B, Daggett V. Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models. Biochemistry. 45: 15573-82. PMID 17176078 DOI: 10.1021/Bi0612723 |
0.638 |
|
| 2006 |
Daggett V. Alpha-sheet: The toxic conformer in amyloid diseases? Accounts of Chemical Research. 39: 594-602. PMID 16981675 DOI: 10.1021/Ar0500719 |
0.395 |
|
| 2006 |
Petrovich M, Jonsson AL, Ferguson N, Daggett V, Fersht AR. Phi-analysis at the experimental limits: mechanism of beta-hairpin formation. Journal of Molecular Biology. 360: 865-81. PMID 16784750 DOI: 10.1016/J.Jmb.2006.05.050 |
0.555 |
|
| 2006 |
Daggett V. Protein folding-simulation. Chemical Reviews. 106: 1898-916. PMID 16683760 DOI: 10.1021/Cr0404242 |
0.478 |
|
| 2006 |
Scott KA, Randles LG, Moran SJ, Daggett V, Clarke J. The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment. Journal of Molecular Biology. 359: 159-73. PMID 16618492 DOI: 10.1016/J.Jmb.2006.03.011 |
0.437 |
|
| 2006 |
Scott KA, Alonso DO, Pan Y, Daggett V. Importance of context in protein folding: secondary structural propensities versus tertiary contact-assisted secondary structure formation. Biochemistry. 45: 4153-63. PMID 16566589 DOI: 10.1021/Bi0517281 |
0.513 |
|
| 2006 |
Rutherford K, Bennion BJ, Parson WW, Daggett V. The 108M polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures. Biochemistry. 45: 2178-88. PMID 16475806 DOI: 10.1021/Bi051988I |
0.782 |
|
| 2005 |
Armen RS, Daggett V. Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology. Biochemistry. 44: 16098-107. PMID 16331970 DOI: 10.1021/Bi050731H |
0.741 |
|
| 2005 |
DeMarco ML, Daggett V. Local environmental effects on the structure of the prion protein. Comptes Rendus Biologies. 328: 847-62. PMID 16286076 DOI: 10.1016/J.Crvi.2005.05.001 |
0.459 |
|
| 2005 |
Armen RS, Bernard BM, Day R, Alonso DO, Daggett V. Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases. Proceedings of the National Academy of Sciences of the United States of America. 102: 13433-8. PMID 16157882 DOI: 10.1073/Pnas.0502068102 |
0.73 |
|
| 2005 |
Day R, Daggett V. Ensemble versus single-molecule protein unfolding. Proceedings of the National Academy of Sciences of the United States of America. 102: 13445-50. PMID 16155127 DOI: 10.1073/Pnas.0501773102 |
0.48 |
|
| 2005 |
White GW, Gianni S, Grossmann JG, Jemth P, Fersht AR, Daggett V. Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding. Journal of Molecular Biology. 350: 757-75. PMID 15967458 DOI: 10.1016/J.Jmb.2005.05.005 |
0.64 |
|
| 2005 |
Jemth P, Day R, Gianni S, Khan F, Allen M, Daggett V, Fersht AR. The structure of the major transition state for folding of an FF domain from experiment and simulation. Journal of Molecular Biology. 350: 363-78. PMID 15935381 DOI: 10.1016/J.Jmb.2005.04.067 |
0.572 |
|
| 2005 |
Day R, Daggett V. Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent. Protein Science : a Publication of the Protein Society. 14: 1242-52. PMID 15840831 DOI: 10.1110/Ps.041226005 |
0.371 |
|
| 2005 |
Ferguson N, Day R, Johnson CM, Allen MD, Daggett V, Fersht AR. Simulation and experiment at high temperatures: ultrafast folding of a thermophilic protein by nucleation-condensation. Journal of Molecular Biology. 347: 855-70. PMID 15769475 DOI: 10.1016/J.Jmb.2004.12.061 |
0.624 |
|
| 2005 |
Esposito L, Daggett V. Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations. Biochemistry. 44: 3358-68. PMID 15736946 DOI: 10.1021/Bi0488350 |
0.436 |
|
| 2005 |
Beck DA, Armen RS, Daggett V. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry. 44: 609-16. PMID 15641786 DOI: 10.1021/Bi0486381 |
0.731 |
|
| 2004 |
Rizzuti B, Daggett V, Guzzi R, Sportelli L. The early steps in the unfolding of azurin. Biochemistry. 43: 15604-9. PMID 15581373 DOI: 10.1021/Bi048685T |
0.462 |
|
| 2004 |
Bennion BJ, DeMarco ML, Daggett V. Preventing misfolding of the prion protein by trimethylamine N-oxide. Biochemistry. 43: 12955-63. PMID 15476389 DOI: 10.1021/Bi0486379 |
0.773 |
|
| 2004 |
Armen RS, Alonso DO, Daggett V. Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH. Structure (London, England : 1993). 12: 1847-63. PMID 15458633 DOI: 10.1016/J.Str.2004.08.005 |
0.729 |
|
| 2004 |
DeMarco ML, Alonso DO, Daggett V. Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein. Journal of Molecular Biology. 341: 1109-24. PMID 15328620 DOI: 10.1016/J.Jmb.2004.06.074 |
0.524 |
|
| 2004 |
Beck DA, Daggett V. Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods (San Diego, Calif.). 34: 112-20. PMID 15283920 DOI: 10.1016/J.Ymeth.2004.03.008 |
0.502 |
|
| 2004 |
Armen RS, DeMarco ML, Alonso DO, Daggett V. Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease. Proceedings of the National Academy of Sciences of the United States of America. 101: 11622-7. PMID 15280548 DOI: 10.1073/Pnas.0401781101 |
0.762 |
|
| 2004 |
Jemth P, Gianni S, Day R, Li B, Johnson CM, Daggett V, Fersht AR. Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. Proceedings of the National Academy of Sciences of the United States of America. 101: 6450-5. PMID 15096617 DOI: 10.1073/Pnas.0401732101 |
0.609 |
|
| 2004 |
Bennion BJ, Daggett V. Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 101: 6433-8. PMID 15096583 DOI: 10.1073/Pnas.0308633101 |
0.768 |
|
| 2004 |
Sato S, Religa TL, Daggett V, Fersht AR. Testing protein-folding simulations by experiment: B domain of protein A. Proceedings of the National Academy of Sciences of the United States of America. 101: 6952-6. PMID 15069202 DOI: 10.1073/Pnas.0401396101 |
0.637 |
|
| 2004 |
DeMarco ML, Daggett V. From conversion to aggregation: protofibril formation of the prion protein. Proceedings of the National Academy of Sciences of the United States of America. 101: 2293-8. PMID 14983003 DOI: 10.1073/Pnas.0307178101 |
0.515 |
|
| 2003 |
Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF, Gai F. Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein. Proceedings of the National Academy of Sciences of the United States of America. 100: 15486-91. PMID 14671331 DOI: 10.1073/Pnas.2136623100 |
0.519 |
|
| 2003 |
Day R, Daggett V. All-atom simulations of protein folding and unfolding. Advances in Protein Chemistry. 66: 373-403. PMID 14631823 DOI: 10.1016/S0065-3233(03)66009-2 |
0.516 |
|
| 2003 |
Gianni S, Guydosh NR, Khan F, Caldas TD, Mayor U, White GW, DeMarco ML, Daggett V, Fersht AR. Unifying features in protein-folding mechanisms. Proceedings of the National Academy of Sciences of the United States of America. 100: 13286-91. PMID 14595026 DOI: 10.1073/Pnas.1835776100 |
0.6 |
|
| 2003 |
Day R, Beck DAC, Armen RS, Daggett V. A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary Protein Science. 12: 2150-2160. PMID 14500873 DOI: 10.1110/Ps.0306803 |
0.734 |
|
| 2003 |
Daggett V, Fersht A. The present view of the mechanism of protein folding. Nature Reviews. Molecular Cell Biology. 4: 497-502. PMID 12778129 DOI: 10.1038/Nrm1126 |
0.602 |
|
| 2003 |
Armen R, Alonso DO, Daggett V. The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions. Protein Science : a Publication of the Protein Society. 12: 1145-57. PMID 12761385 DOI: 10.1110/Ps.0240103 |
0.737 |
|
| 2003 |
Bennion BJ, Daggett V. The molecular basis for the chemical denaturation of proteins by urea Proceedings of the National Academy of Sciences of the United States of America. 100: 5142-5147. PMID 12702764 DOI: 10.1073/Pnas.0930122100 |
0.78 |
|
| 2003 |
Beck DA, Alonso DO, Daggett V. A microscopic view of peptide and protein solvation. Biophysical Chemistry. 100: 221-37. PMID 12646368 DOI: 10.1016/S0301-4622(02)00283-1 |
0.431 |
|
| 2003 |
Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS, Freund SM, Alonso DO, Daggett V, Fersht AR. The complete folding pathway of a protein from nanoseconds to microseconds. Nature. 421: 863-7. PMID 12594518 DOI: 10.1038/Nature01428 |
0.654 |
|
| 2003 |
Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF. The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR. Protein Science : a Publication of the Protein Society. 12: 520-31. PMID 12592022 DOI: 10.1110/Ps.0223003 |
0.344 |
|
| 2003 |
Li B, Daggett V. The molecular basis of the temperature- and pH-induced conformational transitions in elastin-based peptides. Biopolymers. 68: 121-9. PMID 12579584 DOI: 10.1002/Bip.10204 |
0.354 |
|
| 2003 |
Daggett V, Fersht AR. Is there a unifying mechanism for protein folding? Trends in Biochemical Sciences. 28: 18-25. PMID 12517448 DOI: 10.1016/S0968-0004(02)00012-9 |
0.596 |
|
| 2003 |
Biorn AC, Daggett V, DeGrado WF, Dunker AK, Radford SE, Raleigh DP, Rosenblatt M, Urbauer J, Wand AJ. Protein function, folding, and dynamics in the proteinomic era Protein Science. 12: 389-397. |
0.338 |
|
| 2002 |
Alonso DO, An C, 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. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 360: 1165-78. PMID 12804272 DOI: 10.1098/Rsta.2002.0986 |
0.482 |
|
| 2002 |
Li B, Daggett V. Molecular basis for the extensibility of elastin. Journal of Muscle Research and Cell Motility. 23: 561-73. PMID 12785105 DOI: 10.1023/A:1023474909980 |
0.416 |
|
| 2002 |
Bennion BJ, Daggett V. Protein conformation and diagnostic tests: the prion protein. Clinical Chemistry. 48: 2105-14. PMID 12446465 DOI: 10.1093/Clinchem/48.12.2105 |
0.764 |
|
| 2002 |
Day R, Bennion BJ, Ham S, Daggett V. Increasing temperature accelerates protein unfolding without changing the pathway of unfolding Journal of Molecular Biology. 322: 189-203. PMID 12215424 DOI: 10.1016/S0022-2836(02)00672-1 |
0.761 |
|
| 2002 |
Li B, Alonso DO, Daggett V. Stabilization of globular proteins via introduction of temperature-activated elastin-based switches. Structure (London, England : 1993). 10: 989-98. PMID 12121654 DOI: 10.1016/S0969-2126(02)00792-X |
0.391 |
|
| 2002 |
Daggett V. Molecular dynamics simulations of the protein unfolding/folding reaction. Accounts of Chemical Research. 35: 422-9. PMID 12069627 DOI: 10.1021/Ar0100834 |
0.513 |
|
| 2002 |
De Jong D, Riley R, Alonso DO, Daggett V. Probing the energy landscape of protein folding/unfolding transition states. Journal of Molecular Biology. 319: 229-42. PMID 12051948 DOI: 10.1016/S0022-2836(02)00212-7 |
0.457 |
|
| 2002 |
Fersht AR, Daggett V. Protein folding and unfolding at atomic resolution. Cell. 108: 573-82. PMID 11909527 DOI: 10.1016/S0092-8674(02)00620-7 |
0.599 |
|
| 2002 |
Zou Q, Bennion BJ, Daggett V, Murphy KP. The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea. Journal of the American Chemical Society. 124: 1192-202. PMID 11841287 DOI: 10.1021/Ja004206B |
0.747 |
|
| 2002 |
Kazmirski SL, Isaacson RL, An C, Buckle A, Johnson CM, Daggett V, Fersht AR. Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type. Nature Structural Biology. 9: 112-6. PMID 11753432 DOI: 10.1038/Nsb745 |
0.501 |
|
| 2001 |
Main ER, Fulton KF, Daggett V, Jackson SE. A comparison of experimental and computational methods for mapping the interactions present in the transition state for folding of FKBP12. Journal of Biological Physics. 27: 99-117. PMID 23345737 DOI: 10.1023/A:1013137924581 |
0.434 |
|
| 2001 |
Li B, Alonso DOV, Bennion BJ, Daggett V. Hydrophobic hydration is an important source of elasticity in elastin-based biopolymers Journal of the American Chemical Society. 123: 11991-11998. PMID 11724607 DOI: 10.1021/Ja010363E |
0.76 |
|
| 2001 |
Ferguson N, Pires JR, Toepert F, Johnson CM, Pan YP, Volkmer-Engert R, Schneider-Mergener J, Daggett V, Oschkinat H, Fersht A. Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions. Proceedings of the National Academy of Sciences of the United States of America. 98: 13008-13. PMID 11687614 DOI: 10.1073/Pnas.221467398 |
0.629 |
|
| 2001 |
Daggett V. Validation of protein-unfolding transition states identified in molecular dynamics simulations. Biochemical Society Symposium. 83-93. PMID 11573349 DOI: 10.1042/Bss0680083 |
0.503 |
|
| 2001 |
Best RB, Li B, Steward A, Daggett V, Clarke J. Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophysical Journal. 81: 2344-56. PMID 11566804 DOI: 10.1016/S0006-3495(01)75881-X |
0.433 |
|
| 2001 |
Alonso DO, Daggett V. Simulations and computational analyses of prion protein conformations. Advances in Protein Chemistry. 57: 107-37. PMID 11447688 DOI: 10.1016/S0065-3233(01)57020-5 |
0.32 |
|
| 2001 |
Daggett V. Molecular dynamics simulations of protein unfolding/folding. Methods in Molecular Biology (Clifton, N.J.). 168: 215-47. PMID 11357627 DOI: 10.1385/1-59259-193-0:215 |
0.514 |
|
| 2001 |
Ramamurthy V, Tucker C, Wilkie SE, Daggett V, Hunt DM, Hurley JB. Interactions within the coiled-coil domain of RetGC-1 guanylyl cyclase are optimized for regulation rather than for high affinity. The Journal of Biological Chemistry. 276: 26218-29. PMID 11306565 DOI: 10.1074/Jbc.M010495200 |
0.371 |
|
| 2001 |
Kazmirski SL, Wong KB, Freund SM, Tan YJ, Fersht AR, Daggett V. Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 98: 4349-54. PMID 11274353 DOI: 10.1073/Pnas.071054398 |
0.587 |
|
| 2001 |
Pan Y, 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. Biochemistry. 40: 2723-31. PMID 11258883 DOI: 10.1021/Bi0022036 |
0.447 |
|
| 2001 |
Alonso DO, DeArmond SJ, Cohen FE, Daggett V. Mapping the early steps in the pH-induced conformational conversion of the prion protein. Proceedings of the National Academy of Sciences of the United States of America. 98: 2985-9. PMID 11248018 DOI: 10.1073/Pnas.061555898 |
0.421 |
|
| 2001 |
Li B, Alonso DO, Daggett V. The molecular basis for the inverse temperature transition of elastin. Journal of Molecular Biology. 305: 581-92. PMID 11152614 DOI: 10.1006/Jmbi.2000.4306 |
0.364 |
|
| 2001 |
Levitt M, Daggett V. Nature Structural Biology. 8: 662-662. DOI: 10.1038/90356 |
0.364 |
|
| 2000 |
Clarke J, Hounslow AM, Bond CJ, Fersht AR, Daggett V. The effects of disulfide bonds on the denatured state of barnase. Protein Science : a Publication of the Protein Society. 9: 2394-404. PMID 11206061 DOI: 10.1110/Ps.9.12.2394 |
0.559 |
|
| 2000 |
Mayor U, Johnson CM, Daggett V, Fersht AR. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proceedings of the National Academy of Sciences of the United States of America. 97: 13518-22. PMID 11087839 DOI: 10.1073/Pnas.250473497 |
0.553 |
|
| 2000 |
Daggett V. Long timescale simulations. Current Opinion in Structural Biology. 10: 160-4. PMID 10753819 DOI: 10.1016/S0959-440X(00)00062-2 |
0.441 |
|
| 2000 |
Wong KB, Clarke J, Bond CJ, Neira JL, Freund SM, Fersht AR, Daggett V. Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. Journal of Molecular Biology. 296: 1257-82. PMID 10698632 DOI: 10.1006/Jmbi.2000.3523 |
0.581 |
|
| 2000 |
Alonso DO, Alm E, Daggett V. Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping. Structure (London, England : 1993). 8: 101-10. PMID 10673427 DOI: 10.1016/S0969-2126(00)00083-6 |
0.4 |
|
| 2000 |
Alonso DO, Daggett V. Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains. Proceedings of the National Academy of Sciences of the United States of America. 97: 133-8. PMID 10618383 DOI: 10.1073/Pnas.97.1.133 |
0.397 |
|
| 1999 |
Fulton KF, Main ER, Daggett V, Jackson SE. Mapping the interactions present in the transition state for unfolding/folding of FKBP12. Journal of Molecular Biology. 291: 445-61. PMID 10438631 DOI: 10.1006/Jmbi.1999.2942 |
0.42 |
|
| 1999 |
Kazmirski SL, Li A, Daggett V. Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. Journal of Molecular Biology. 290: 283-304. PMID 10388573 DOI: 10.1006/Jmbi.1999.2843 |
0.519 |
|
| 1999 |
Storch EM, Grinstead JS, Campbell AP, Daggett V, Atkins WM. Engineering out motion: a surface disulfide bond alters the mobility of tryptophan 22 in cytochrome b5 as probed by time-resolved fluorescence and 1H NMR experiments. Biochemistry. 38: 5065-75. PMID 10213609 DOI: 10.1021/Bi982159I |
0.377 |
|
| 1999 |
Storch EM, Daggett V, Atkins WM. Engineering out motion: introduction of a de novo disulfide bond and a salt bridge designed to close a dynamic cleft on the surface of cytochrome b5. Biochemistry. 38: 5054-64. PMID 10213608 DOI: 10.1021/Bi982158Q |
0.441 |
|
| 1998 |
Daggett V. Structure-function aspects of prion proteins. Current Opinion in Biotechnology. 9: 549. PMID 9831523 DOI: 10.1016/S0958-1669(98)80008-6 |
0.453 |
|
| 1998 |
Kazmirski SL, Daggett V. Non-native interactions in protein folding intermediates: Molecular dynamics simulations of hen lysozyme Journal of Molecular Biology. 284: 793-806. PMID 9826516 DOI: 10.1006/Jmbi.1998.2192 |
0.519 |
|
| 1998 |
Wong KB, Daggett V. Barstar has a highly dynamic hydrophobic core: evidence from molecular dynamics simulations and nuclear magnetic resonance relaxation data. Biochemistry. 37: 11182-92. PMID 9698364 DOI: 10.1021/Bi980552I |
0.419 |
|
| 1998 |
Ladurner AG, Itzhaki LS, Daggett V, Fersht AR. Synergy between simulation and experiment in describing the energy landscape of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 95: 8473-8. PMID 9671702 DOI: 10.1073/Pnas.95.15.8473 |
0.65 |
|
| 1998 |
Alonso DOV, Daggett V. Molecular dynamics simulations of hydrophobic collapse of ubiquitin Protein Science. 7: 860-874. PMID 9568893 DOI: 10.1002/Pro.5560070404 |
0.515 |
|
| 1998 |
Kazmirski SL, Daggett V. Simulations of the structural and dynamical properties of denatured proteins: The 'Molten Coil' state of bovine pancreatic trypsin inhibitor Journal of Molecular Biology. 277: 487-506. PMID 9514766 DOI: 10.1006/Jmbi.1998.1634 |
0.526 |
|
| 1998 |
Li A, Daggett V. Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate Journal of Molecular Biology. 275: 677-694. PMID 9466940 DOI: 10.1006/Jmbi.1997.1484 |
0.473 |
|
| 1998 |
Daggett V, Li A, Fersht AR. Combined molecular dynamics and Φ-value analysis of structure- reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects Journal of the American Chemical Society. 120: 12740-12754. DOI: 10.1021/Ja981558Y |
0.453 |
|
| 1998 |
Li Z, Laidig KE, Daggett V. Conformational search using a molecular dynamics-minimization procedure: Applications to clusters of coulombic charges, Lennard-Jones particles, and waters Journal of Computational Chemistry. 19: 60-70. DOI: 10.1002/(Sici)1096-987X(19980115)19:1<60::Aid-Jcc5>3.0.Co;2-X |
0.31 |
|
| 1997 |
Bond CJ, Wong KB, Clarke J, Fersht AR, Daggett V. Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. Proceedings of the National Academy of Sciences of the United States of America. 94: 13409-13. PMID 9391038 DOI: 10.1073/Pnas.94.25.13409 |
0.614 |
|
| 1997 |
Harrison PM, Bamborough P, Daggett V, Prusiner SB, Cohen FE. The prion folding problem. Current Opinion in Structural Biology. 7: 53-9. PMID 9032055 DOI: 10.1016/S0959-440X(97)80007-3 |
0.401 |
|
| 1997 |
Levitt M, Hirshberg M, Sharon R, Laidig KE, Daggett V. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution Journal of Physical Chemistry B. 101: 5051-5061. DOI: 10.1021/Jp964020S |
0.511 |
|
| 1997 |
Kazmirski SL, Daggett V. Protein Dynamics: A Theoretical Perspective Advances in Molecular and Cell Biology. 22: 339-390. DOI: 10.1016/S1569-2558(08)60481-6 |
0.462 |
|
| 1996 |
Laidig KE, Daggett V. Molecular dynamics simulations of apocytochrome b562 - The highly ordered limit of molten globules Folding and Design. 1: 335-346. PMID 9080180 DOI: 10.1016/S1359-0278(96)00049-1 |
0.403 |
|
| 1996 |
Storch EM, Daggett V. Structural consequences of heme removal: Molecular dynamics simulations of rat and bovine apocytochrome b5 Biochemistry. 35: 11596-11604. PMID 8794739 DOI: 10.1021/Bi960598G |
0.429 |
|
| 1996 |
Daggett V, Li A, Itzhaki LS, Otzen DE, Fersht AR. Structure of the transition state for folding of a protein derived from experiment and simulation. Journal of Molecular Biology. 257: 430-40. PMID 8609634 DOI: 10.1006/Jmbi.1996.0173 |
0.608 |
|
| 1996 |
Li A, Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations Journal of Molecular Biology. 257: 412-429. PMID 8609633 DOI: 10.1006/Jmbi.1996.0172 |
0.456 |
|
| 1996 |
Laidig KE, Daggett V. Testing the modified hydration-shell hydrogen-bond model of hydrophobic effects using molecular dynamics simulation Journal of Physical Chemistry. 100: 5616-5619. DOI: 10.1021/Jp960520+ |
0.341 |
|
| 1996 |
Kazmirski SL, Alonso DOV, Cohen FE, Prusiner SB, Daggett V. The conformational consequences of mutations to the H1 helix of the prion protein explored by molecular dynamics simulations Techniques in Protein Chemistry. 7: 469-477. DOI: 10.1016/S1080-8914(96)80051-2 |
0.498 |
|
| 1995 |
Kazmirski SL, Alonso DO, Cohen FE, Prusiner SB, Daggett V. Theoretical studies of sequence effects on the conformational properties of a fragment of the prion protein: implications for scrapie formation. Chemistry & Biology. 2: 305-15. PMID 9383432 DOI: 10.1016/1074-5521(95)90049-7 |
0.455 |
|
| 1995 |
Li A, Daggett V. Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: Comparison to x-ray crystallographic and nmr data Protein Engineering, Design and Selection. 8: 1117-1128. PMID 8819977 DOI: 10.1093/Protein/8.11.1117 |
0.449 |
|
| 1995 |
Kirshenbaum K, Daggett V. Sequence effects on the conformational properties of the amyloid β(1-28) peptide: Testing a proposed mechanism for the α → β transition Biochemistry. 34: 7640-7647. PMID 7779810 DOI: 10.1021/Bi00023A010 |
0.406 |
|
| 1995 |
Kirshenbaum K, Daggett V. pH-dependent conformations of the amyloid β(1-28) peptide fragment explored using molecular dynamics Biochemistry. 34: 7629-7639. PMID 7779809 DOI: 10.1021/Bi00023A009 |
0.388 |
|
| 1995 |
Alonso DOV, Daggett V. Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding: Characterization of Partially Unfolded States of Ubiquitin in 60% Methanol and in Water Journal of Molecular Biology. 247: 501-520. PMID 7714903 DOI: 10.1006/Jmbi.1994.0156 |
0.481 |
|
| 1995 |
Storch EM, Daggett V. Molecular dynamics simulation of cytochrome b5: Implications for protein-protein recognition Biochemistry. 34: 9682-9693. PMID 7626638 DOI: 10.1021/Bi00030A005 |
0.516 |
|
| 1995 |
Levitt M, Hirshberg M, Sharon R, Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Computer Physics Communications. 91: 215-231. DOI: 10.1016/0010-4655(95)00049-L |
0.538 |
|
| 1994 |
Li A, Daggett V. Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proceedings of the National Academy of Sciences of the United States of America. 91: 10430-4. PMID 7937969 DOI: 10.1073/Pnas.91.22.10430 |
0.457 |
|
| 1994 |
Daggett V, Levitt M. Protein folding↔unfolding dynamics Current Opinion in Structural Biology. 4: 291-295. DOI: 10.1016/S0959-440X(94)90322-0 |
0.625 |
|
| 1993 |
Daggett V, Levitt M. Realistic simulations of native-protein dynamics in solution and beyond. Annual Review of Biophysics and Biomolecular Structure. 22: 353-80. PMID 8347994 DOI: 10.1146/Annurev.Bb.22.060193.002033 |
0.581 |
|
| 1993 |
Daggett V, Levitt M. Protein unfolding pathways explored through molecular dynamics simulations. Journal of Molecular Biology. 232: 600-19. PMID 7688428 DOI: 10.1006/Jmbi.1993.1414 |
0.637 |
|
| 1993 |
Daggett V. A Model for the Molten Globule State of CTF Generated Using Molecular Dynamics Techniques in Protein Chemistry. 525-532. DOI: 10.1016/B978-0-12-058757-5.50062-7 |
0.505 |
|
| 1992 |
Daggett V, Levitt M. A model of the molten globule state from molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 89: 5142-6. PMID 1594623 DOI: 10.1073/Pnas.89.11.5142 |
0.642 |
|
| 1992 |
Daggett V, Levitt M. Molecular dynamics simulations of helix denaturation. Journal of Molecular Biology. 223: 1121-38. PMID 1538392 DOI: 10.1016/0022-2836(92)90264-K |
0.55 |
|
| 1991 |
Daggett V, Kollman PA, Kuntz ID. Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers. 31: 285-304. PMID 1868159 DOI: 10.1002/Bip.360310304 |
0.648 |
|
| 1991 |
Kollman PA, Daggett V, Dang LX. The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme. Ciba Foundation Symposium. 161: 91-103; discussion 1. PMID 1814699 |
0.441 |
|
| 1991 |
Daggett V, Kollman PA, Kuntz ID. A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers. 31: 1115-34. PMID 1786342 DOI: 10.1002/Bip.360310911 |
0.709 |
|
| 1991 |
Daggett V, Schroeder S, Kollman P. Catalytic pathway of serine proteases: classical and quantum mechanical calculations Journal of the American Chemical Society. 113: 8926-8935. DOI: 10.1021/Ja00023A047 |
0.435 |
|
| 1991 |
Schroeder S, Daggett V, Kollman P. A comparison of the AM1 and PM3 semiempirical models for evaluating model compounds relevant to catalysis by serine proteases Journal of the American Chemical Society. 113: 8922-8925. DOI: 10.1021/Ja00023A046 |
0.431 |
|
| 1991 |
Daggett V, Levitt M. A molecular dynamics simulation of the C-terminal fragment of the L7/L12 ribosomal protein in solution Chemical Physics. 158: 501-512. DOI: 10.1016/0301-0104(91)87085-A |
0.449 |
|
| 1990 |
Daggett V, Kollman PA. Molecular dynamics simulations of active site mutants of triosephosphate isomerase. Protein Engineering. 3: 677-90. PMID 2217142 DOI: 10.1093/Protein/3.8.677 |
0.471 |
|
| 1989 |
Daggett V, Brown F, Kollman P. Free energy component analysis: a study of the glutamic acid 165 .fwdarw. aspartic acid 165 mutation in triosephosphate isomerase Journal of the American Chemical Society. 111: 8247-8256. DOI: 10.1021/Ja00203A028 |
0.431 |
|
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