Dynameomics: a comprehensive database of protein dynamics.

[1]  Rudesh D. Toofanny,et al.  A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding. , 2010, Biophysical journal.

[2]  K. Gardner,et al.  Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B. , 2009, Journal of the American Chemical Society.

[3]  Valerie Daggett,et al.  Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. , 2009, Biophysical journal.

[4]  V. Daggett,et al.  The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface. , 2009, Protein engineering, design & selection : PEDS.

[5]  B. Kennedy,et al.  Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V. , 2009, Biophysical journal.

[6]  Russ B Altman,et al.  Improving structure-based function prediction using molecular dynamics. , 2009, Structure.

[7]  V. Daggett,et al.  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. , 2009, Journal of the American Chemical Society.

[8]  V. Daggett,et al.  A hotspot of inactivation: The A22S and V108M polymorphisms individually destabilize the active site structure of catechol O-methyltransferase. , 2009, Biochemistry.

[9]  Dan S. Tawfik,et al.  Protein Dynamism and Evolvability , 2009, Science.

[10]  Lila M. Gierasch,et al.  Sending Signals Dynamically , 2009, Science.

[11]  C. Craik,et al.  Trapping Moving Targets with Small Molecules , 2009, Science.

[12]  Jeffrey W. Peng.  Communication breakdown: protein dynamics and drug design. , 2009, Structure.

[13]  Andrew L. Lee,et al.  Dynamic dysfunction in dihydrofolate reductase results from antifolate drug binding: modulation of dynamics within a structural state. , 2009, Structure.

[14]  Michele Vendruscolo,et al.  The Mechanism of Folding of Im7 Reveals Competition between Functional and Kinetic Evolutionary Constraints , 2009, Nature Structural &Molecular Biology.

[15]  Modesto Orozco,et al.  An atomistic view to the gas phase proteome. , 2009, Structure.

[16]  Christopher J. Woods,et al.  Biomolecular simulation and modelling: status, progress and prospects , 2008, Journal of The Royal Society Interface.

[17]  Valerie Daggett,et al.  Dynameomics: Large‐scale assessment of native protein flexibility , 2008, Protein science : a publication of the Protein Society.

[18]  Ian Sillitoe,et al.  The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies , 2008, Nucleic Acids Res..

[19]  V. Daggett,et al.  Molecular basis for the structural instability of human DJ-1 induced by the L166P mutation associated with Parkinson's disease. , 2008, Biochemistry.

[20]  Valerie Daggett,et al.  The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins , 2008, Proceedings of the National Academy of Sciences.

[21]  Frank M Boeckler,et al.  Targeted rescue of a destabilized mutant of p53 by an in silico screened drug , 2008, Proceedings of the National Academy of Sciences.

[22]  David A. C. Beck,et al.  Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain. , 2008, Biochemistry.

[23]  W. W. Parson,et al.  Crystal structures of human 108V and 108M catechol O-methyltransferase. , 2008, Journal of molecular biology.

[24]  V. Daggett,et al.  Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics. , 2008, Journal of molecular biology.

[25]  R Dustin Schaeffer,et al.  Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. , 2008, Protein engineering, design & selection : PEDS.

[26]  Valerie Daggett,et al.  Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data. , 2008, Protein engineering, design & selection : PEDS.

[27]  Valerie Daggett,et al.  Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. , 2008, Protein engineering, design & selection : PEDS.

[28]  Chie Motono,et al.  Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: A structural and dynamic analysis , 2008, Proteins.

[29]  A. Fersht,et al.  Combining experiment and simulation in protein folding: closing the gap for small model systems. , 2008, Current opinion in structural biology.

[30]  V. Daggett,et al.  The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics. , 2008, Biochemistry.

[31]  David A C Beck,et al.  A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. , 2007, Biophysical journal.

[32]  A. Fersht,et al.  Conformational entropy of alanine versus glycine in protein denatured states , 2007, Proceedings of the National Academy of Sciences.

[33]  Ryan Day,et al.  Direct observation of microscopic reversibility in single-molecule protein folding. , 2007, Journal of molecular biology.

[34]  Modesto Orozco,et al.  A consensus view of protein dynamics , 2007, Proceedings of the National Academy of Sciences.

[35]  Werner Dubitzky,et al.  P-found: The Protein Folding and Unfolding Simulation Repository , 2006, 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

[36]  C. Dobson,et al.  Protein misfolding, functional amyloid, and human disease. , 2006, Annual review of biochemistry.

[37]  Jonathan W. Essex,et al.  BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis , 2006, Future Gener. Comput. Syst..

[38]  Valerie Daggett,et al.  Protein folding-simulation. , 2006, Chemical reviews.

[39]  Kang Chen,et al.  Conformation of the backbone in unfolded proteins. , 2006, Chemical reviews.

[40]  V. Daggett,et al.  The 108M polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures. , 2006, Biochemistry.

[41]  J. Moult,et al.  Loss of protein structure stability as a major causative factor in monogenic disease. , 2005, Journal of molecular biology.

[42]  Jonathan W. Essex,et al.  BioSimGrid: A distributed environment for archiving and the analysis of biomolecular simulations , 2005 .

[43]  Abhishek K. Jha,et al.  Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. , 2005, Biochemistry.

[44]  Guy L. Steele,et al.  Java(TM) Language Specification, The (3rd Edition) (Java (Addison-Wesley)) , 2005 .

[45]  M. Karplus,et al.  Molecular dynamics and protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[46]  David A. C. Beck,et al.  Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. , 2005, Biochemistry.

[47]  David A C Beck,et al.  Methods for molecular dynamics simulations of protein folding/unfolding in solution. , 2004, Methods.

[48]  M. Karplus,et al.  The origin of protein sidechain order parameter distributions. , 2004, Journal of the American Chemical Society.

[49]  Jorng-Tzong Horng,et al.  PGTdb: a database providing growth temperatures of prokaryotes , 2004, Bioinform..

[50]  Ryan Day,et al.  A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary , 2003, Protein science : a publication of the Protein Society.

[51]  Patrice Koehl,et al.  The ASTRAL Compendium in 2004 , 2003, Nucleic Acids Res..

[52]  Valerie Daggett,et al.  The present view of the mechanism of protein folding , 2003, Nature Reviews Molecular Cell Biology.

[53]  Valerie Daggett,et al.  The complete folding pathway of a protein from nanoseconds to microseconds , 2003, Nature.

[54]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[55]  Roland L. Dunbrack.  Rotamer libraries in the 21st century. , 2002, Current opinion in structural biology.

[56]  V. Daggett.  Molecular dynamics simulations of the protein unfolding/folding reaction. , 2002, Accounts of chemical research.

[57]  Sheena E. Radford,et al.  Im7 folding mechanism: misfolding on a path to the native state , 2002, Nature Structural Biology.

[58]  A. Fersht,et al.  Protein Folding and Unfolding at Atomic Resolution , 2002, Cell.

[59]  Liisa Holm,et al.  Identification of homology in protein structure classification , 2001, Nature Structural Biology.

[60]  J. Moult,et al.  SNPs, protein structure, and disease , 2001, Human mutation.

[61]  C. Vieille,et al.  Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability , 2001, Microbiology and Molecular Biology Reviews.

[62]  D. LeMaster,et al.  From the Cover: Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature , 2000 .

[63]  Kenneth M. Merz,et al.  Stability and Activity of Mesophilic Subtilisin E and Its Thermophilic Homolog: Insights from Molecular Dynamics Simulations , 1999 .

[64]  S. Kazmirski,et al.  Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. , 1999, Journal of molecular biology.

[65]  Valerie Daggett,et al.  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 , 1998 .

[66]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[67]  V. Daggett,et al.  Barstar has a highly dynamic hydrophobic core: evidence from molecular dynamics simulations and nuclear magnetic resonance relaxation data. , 1998, Biochemistry.

[68]  A. Fersht,et al.  Synergy between simulation and experiment in describing the energy landscape of protein folding. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[69]  C L Brooks,et al.  Calculations on folding of segment B1 of streptococcal protein G. , 1998, Journal of molecular biology.

[70]  M Karplus,et al.  Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin , 1997, Protein science : a publication of the Protein Society.

[71]  Roland L. Dunbrack,et al.  Bayesian statistical analysis of protein side‐chain rotamer preferences , 1997, Protein science : a publication of the Protein Society.

[72]  Michael Levitt,et al.  Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution , 1997 .

[73]  Guy L. Steele,et al.  The Java Language Specification , 1996 .

[74]  A. Li,et al.  Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. , 1996, Journal of molecular biology.

[75]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[76]  M. Levitt,et al.  Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution , 1995 .

[77]  M. Swindells,et al.  Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures , 1995, Nature Structural Biology.

[78]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[79]  A. Li,et al.  Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[80]  A. Szabó,et al.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity , 1982 .

[81]  R. Leighton,et al.  Feynman Lectures on Physics , 1971 .

[82]  S. Krimm,et al.  Circular dichroism of poly-L-proline in an unordered conformation. , 1968, Biopolymers.

[83]  Alan R Davidson,et al.  The structure of “unstructured” regions in peptides and proteins: Role of the polyproline II helix in protein folding and recognition * , 2005, Biopolymers.

[84]  Lydia E. Kavraki,et al.  Understanding Protein Flexibility through Dimensionality Reduction , 2003, J. Comput. Biol..

[85]  Robert W Woody,et al.  Is polyproline II a major backbone conformation in unfolded proteins? , 2002, Advances in protein chemistry.

[86]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[87]  M. Swindells,et al.  Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. , 1995, Nature structural biology.

[88]  Samuel Krimm,et al.  The Circular Dichroism Spectrum and Structure of Unordered Polypeptides and Proteins , 1974 .

[89]  H. Berman,et al.  Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank , 2022 .