Molecules in motion: Computing structural flexibility

[1]  Chaok Seok,et al.  A kinematic view of loop closure , 2004, J. Comput. Chem..

[2]  K. Diederichs,et al.  The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution. , 1991, Journal of molecular biology.

[3]  Mariusz Milik,et al.  Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates , 1997 .

[4]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[5]  Bernard Roth,et al.  Kinematic analysis of the 6R manipulator of general geometry , 1991 .

[6]  B. Hess.  Convergence of sampling in protein simulations. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[7]  Nancy M. Amato,et al.  Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures , 2003, J. Comput. Biol..

[8]  M. Levitt.  Accurate modeling of protein conformation by automatic segment matching. , 1992, Journal of molecular biology.

[9]  Norelle L Daly,et al.  Engineering stable peptide toxins by means of backbone cyclization: stabilization of the alpha-conotoxin MII. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Obradovic,et al.  Predicting Protein Disorder for N-, C-, and Internal Regions. , 1999, Genome informatics. Workshop on Genome Informatics.

[11]  A. Fersht,et al.  Contribution of residues in the reactive site loop of chymotrypsin inhibitor 2 to protein stability and activity. , 1994, Biochemistry.

[12]  A. Bax,et al.  Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. , 1997, Science.

[13]  D A Agard,et al.  Kinetics versus thermodynamics in protein folding. , 1994, Biochemistry.

[14]  R. Unger,et al.  Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications. , 1993, Bulletin of mathematical biology.

[15]  Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing. , 2004, Biochemistry.

[16]  Wei Zhang,et al.  A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..

[17]  E. Schrödinger,et al.  What is life? : the physical aspect of the living cell , 1946 .

[18]  Ad Bax,et al.  Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. , 2003, Journal of the American Chemical Society.

[19]  U. Hansmann.  Parallel tempering algorithm for conformational studies of biological molecules , 1997, physics/9710041.

[20]  M. Karplus,et al.  Conformational sampling using high‐temperature molecular dynamics , 1990, Biopolymers.

[21]  M. DePristo,et al.  Simultaneous determination of protein structure and dynamics , 2005, Nature.

[22]  E. Primrose.  On the input-output equation of the general 7R-mechanism , 1986 .

[23]  Cecilia Clementi,et al.  Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. , 2004, Journal of the American Chemical Society.

[24]  C. Deane,et al.  A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins , 2000, Proteins.

[25]  G. Schulz,et al.  Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. , 1996, Journal of molecular biology.

[26]  D. Fushman,et al.  Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G , 2003, Journal of biomolecular NMR.

[27]  A. Liwo,et al.  Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Robert E. Bruccoleri,et al.  Application of Systematic Conformational Search to Protein Modeling , 1993 .

[29]  V. Muñoz,et al.  Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.

[30]  Ad Bax,et al.  Insights into the mobility of methyl-bearing side chains in proteins from (3)J(CC) and (3)J(CN) couplings. , 2003, Journal of the American Chemical Society.

[31]  Jiří Novotný,et al.  Structure of antibody hypervariable loops reproduced by a conformational search algorithm , 1988, Nature.

[32]  L Serrano,et al.  Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. , 1997, Biopolymers.

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

[34]  Nathan A. Baker,et al.  Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Wang,et al.  Replica Monte Carlo simulation of spin glasses. , 1986, Physical review letters.

[36]  Wilfred F van Gunsteren,et al.  Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.

[37]  C. Levinthal,et al.  Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures , 1987, Biopolymers.

[38]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[39]  Peter G. Wolynes,et al.  Biomolecules: Where the Physics of Complexity and Simplicity Meet , 1994 .

[40]  Andrej Sali,et al.  Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. , 2006, Journal of molecular biology.

[41]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[42]  R. Levy,et al.  Protein dynamics and NMR relaxation: comparison of simulations with experiment , 1982, Nature.

[43]  Ruben Abagyan,et al.  ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..

[44]  Steven Hayward,et al.  Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions , 2007, Proteins.

[45]  N. Go,et al.  Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. , 2009 .

[46]  Anil K. Jain,et al.  Bootstrap Techniques for Error Estimation , 1987, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[47]  Julian Tirado-Rives,et al.  Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Guoli Wang,et al.  PISCES: a protein sequence culling server , 2003, Bioinform..

[49]  S. Forsén,et al.  Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography. , 1992, Journal of Molecular Biology.

[50]  John P. Overington,et al.  Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. , 1993, Journal of molecular biology.

[51]  Harold A. Scheraga,et al.  Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability‐directed search procedure , 1989 .

[52]  A. Means,et al.  Molecular mechanisms of action of calmodulin. , 1988, Recent progress in hormone research.

[53]  S Vajda,et al.  Determining protein loop conformation using scaling‐relaxation techniques , 1993, Protein science : a publication of the Protein Society.

[54]  Cecilia Clementi,et al.  Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Ad Bax,et al.  Solution structure of calcium-free calmodulin , 1995, Nature Structural Biology.

[56]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[57]  D. Chandler,et al.  Introduction To Modern Statistical Mechanics , 1987 .

[58]  Alan M. Ferrenberg,et al.  Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.

[59]  N. Isern,et al.  Structure and DNA-binding Sites of the SWI1 AT-rich Interaction Domain (ARID) Suggest Determinants for Sequence-specific DNA Recognition* , 2004, Journal of Biological Chemistry.

[60]  T F Havel,et al.  The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X‐ray structures , 1992, Protein science : a publication of the Protein Society.

[61]  Alexander Y. Grosberg,et al.  Giant Molecules: Here, There, and Everywhere , 1997 .

[62]  D G Rhoads,et al.  Initial velocity and equilibrium kinetics of myokinase. , 1968, The Journal of biological chemistry.

[63]  J A McCammon,et al.  Anti‐insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent , 1992, Biopolymers.

[64]  Richard Bonneau,et al.  Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.

[65]  L. Kay,et al.  Intrinsic dynamics of an enzyme underlies catalysis , 2005, Nature.

[66]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[67]  Harold A. Scheraga,et al.  Pattern recognition in the prediction of protein structure. III. An importance‐sampling minimization procedure , 1989 .

[68]  A. Fersht.  Structure and mechanism in protein science , 1998 .

[69]  Cecilia Clementi,et al.  Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go? , 2004, Journal of molecular biology.

[70]  J. Ponder,et al.  Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions , 1998 .

[71]  A. Fersht,et al.  Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. , 1993, Biochemistry.

[72]  D I Stuart,et al.  Alpha-lactalbumin possesses a distinct zinc binding site. , 1995, The Journal of biological chemistry.

[73]  Dinesh Manocha,et al.  Kinematic Manipulation of Molecular Chains Subject to Rigid Constraint , 1994, ISMB.

[74]  L. Kavraki,et al.  Multiscale characterization of protein conformational ensembles , 2009, Proteins.

[75]  S. Reissmann,et al.  Conformational properties of a cyclic peptide bradykinin B2 receptor antagonist using experimental and theoretical methods. , 2000, The journal of peptide research : official journal of the American Peptide Society.

[76]  L. Björck,et al.  Streptococcal protein G. Gene structure and protein binding properties. , 1991, The Journal of biological chemistry.

[77]  I. Bahar,et al.  Normal mode analysis : theory and applications to biological and chemical systems , 2005 .

[78]  Oussama Khatib,et al.  Operational space dynamics: efficient algorithms for modeling and control of branching mechanisms , 2000, Proceedings 2000 ICRA. Millennium Conference. IEEE International Conference on Robotics and Automation. Symposia Proceedings (Cat. No.00CH37065).

[79]  L. Lai,et al.  Protein loops on structurally similar scaffolds: database and conformational analysis. , 1999, Biopolymers.

[80]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[81]  I D Campbell,et al.  Solution structure and peptide binding of the SH3 domain from human Fyn. , 1996, Structure.

[82]  C. Pickart.  ReviewBack to the Future with Ubiquitin be eliminated for purposes of regulation or quality con - , 2004 .

[83]  S. Christakos,et al.  Vitamin D-dependent calcium binding proteins: chemistry, distribution, functional considerations, and molecular biology. , 1989, Endocrine reviews.

[84]  Harold A. Scheraga,et al.  Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops , 1990 .

[85]  G. Schulz,et al.  Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. , 1996, Structure.

[86]  J. Onuchic,et al.  How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[87]  David A. Lee,et al.  Predicting protein function from sequence and structure , 2007, Nature Reviews Molecular Cell Biology.

[88]  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.

[89]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[90]  N. Mousseau,et al.  Dynamics of lennard-jones clusters: A characterization of the activation-relaxation technique , 2000 .

[91]  V. Hilser,et al.  Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. , 1996, Journal of molecular biology.

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

[93]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[94]  David J. Craik,et al.  Seamless Proteins Tie Up Their Loose Ends , 2006, Science.

[95]  P. Bradley,et al.  Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.

[96]  P. Wolynes,et al.  Water in protein structure prediction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[97]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[98]  Louis Carlacci,et al.  Loop problem in proteins: Developments on Monte Carlo simulated annealing approach , 1996 .

[99]  A. Rayan,et al.  Exploring the conformational space of cyclic peptides by a stochastic search method. , 2004, Journal of molecular graphics & modelling.

[100]  F. Baneyx,et al.  Recombinant protein folding and misfolding in Escherichia coli , 2004, Nature Biotechnology.

[101]  Thierry Siméon,et al.  A path planning approach for computing large-amplitude motions of flexible molecules , 2005, ISMB.

[102]  D. Kern,et al.  The role of dynamics in allosteric regulation. , 2003, Current opinion in structural biology.

[103]  V. Daggett,et al.  Long timescale simulations. , 2000, Current opinion in structural biology.

[104]  Lydia E. Kavraki,et al.  Randomized path planning for linkages with closed kinematic chains , 2001, IEEE Trans. Robotics Autom..

[105]  Rafael Brüschweiler,et al.  Prediction of methyl-side Chain Dynamics in Proteins , 2004, Journal of biomolecular NMR.

[106]  G Vasmatzis,et al.  Predicting immunoglobulin‐like hypervariable loops , 1994, Biopolymers.

[107]  A Tramontano,et al.  Conformations of the third hypervariable region in the VH domain of immunoglobulins. , 1998, Journal of molecular biology.

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

[109]  D. Baker,et al.  Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.

[110]  Barry Honig,et al.  Extending the accuracy limits of prediction for side-chain conformations. , 2001 .

[111]  Eva Thulin,et al.  Calcium-induced structural changes and domain autonomy in calmodulin , 1995, Nature Structural Biology.

[112]  Zhijian J. Chen,et al.  The novel functions of ubiquitination in signaling. , 2004, Current opinion in cell biology.

[113]  R. Abagyan,et al.  Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop. , 1997, Protein engineering.

[114]  P. Romero,et al.  Sequence complexity of disordered protein , 2001, Proteins.

[115]  Robert E. Bruccoleri,et al.  Chain closure with bond angle variations , 1985 .

[116]  A V Finkelstein,et al.  Search for the stable state of a short chain in a molecular field. , 1992, Protein engineering.

[117]  G. Schulz,et al.  High‐resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer , 1995, Protein science : a publication of the Protein Society.

[118]  Harold A. Scheraga,et al.  Standard‐geometry chains fitted to X‐ray derived structures: Validation of the rigid‐geometry approximation. I. Chain closure through a limited search of “loop” conformations , 1991 .

[119]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[120]  Eckart Bindewald,et al.  A divide and conquer approach to fast loop modeling. , 2002, Protein engineering.

[121]  Jean-Claude Latombe,et al.  Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion , 2003, J. Comput. Biol..

[122]  Ad Bax,et al.  Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase , 1998 .

[123]  J. Onuchic,et al.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. , 2000, Journal of molecular biology.

[124]  Jan Verschelde,et al.  Advances in Polynomial Continuation for Solving Problems in Kinematics , 2004 .

[125]  Oliver Brock,et al.  Elastic Strips: A Framework for Motion Generation in Human Environments , 2002, Int. J. Robotics Res..

[126]  W. Chazin,et al.  Determination of the solution structure of Apo calbindin D9k by NMR spectroscopy. , 1995, Journal of molecular biology.

[127]  M. Delaforge,et al.  Predicting the conformational states of cyclic tetrapeptides. , 2003, Biopolymers.

[128]  Jonathan Boyd,et al.  The three-dimensional structure of the tenth type III module of fibronectin: An insight into RGD-mediated interactions , 1992, Cell.

[129]  Eleanor J. Dodson,et al.  Computational biology: Protein predictions , 2007, Nature.

[130]  Johannes Buchner,et al.  Protein folding handbook , 2005 .

[131]  Jean Garnier,et al.  Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins , 1992, Biopolymers.

[132]  R C Brower,et al.  Exhaustive conformational search and simulated annealing for models of lattice peptides , 1993, Biopolymers.

[133]  D. Craik,et al.  Three-dimensional structure of RTD-1, a cyclic antimicrobial defensin from Rhesus macaque leukocytes. , 2001, Biochemistry.

[134]  L. Björck,et al.  Differences in backbone dynamics of two homologous bacterial albumin-binding modules: implications for binding specificity and bacterial adaptation. , 2002, Journal of molecular biology.

[135]  V. Pande,et al.  Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. , 2006, The Journal of chemical physics.

[136]  Qiang Lu,et al.  Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles. , 2008, Journal of the American Chemical Society.

[137]  Yoshihide Hayashizaki,et al.  Sharing genomes: an integrated approach to funding, managing and distributing genomic clone resources , 2004, Nature Reviews Genetics.

[138]  C. Brooks,et al.  Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models , 2000 .

[139]  Ron Elber,et al.  Long-timescale simulation methods. , 2005, Current opinion in structural biology.

[140]  J. Moult,et al.  Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms , 1995, Proteins.

[141]  Lauren Wickstrom,et al.  Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. , 2007, The journal of physical chemistry. B.

[142]  Cecilia Clementi,et al.  Minimalist protein model as a diagnostic tool for misfolding and aggregation. , 2006, Journal of molecular biology.

[143]  J. Onuchic,et al.  Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations , 2006, Proceedings of the National Academy of Sciences.

[144]  A. Lesk,et al.  Common features of the conformations of antigen‐binding loops in immunoglobulins and application to modeling loop conformations , 1992, Proteins.

[145]  Stewart A. Adcock,et al.  Molecular dynamics: survey of methods for simulating the activity of proteins. , 2006, Chemical reviews.

[146]  C D Kroenke,et al.  Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. , 2001, Methods in enzymology.

[147]  J. Skolnick,et al.  MONSSTER: a method for folding globular proteins with a small number of distance restraints. , 1997, Journal of molecular biology.

[148]  Harold A Scheraga,et al.  Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. , 2004, Journal of molecular biology.

[149]  Itay Lotan,et al.  Algorithms exploiting the chain structure of proteins , 2004 .

[150]  T. Blundell,et al.  Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling. , 1997, Journal of molecular biology.

[151]  Bruce J. Berne,et al.  Multicanonical jump walking: A method for efficiently sampling rough energy landscapes , 1999 .

[152]  C. Levinthal,et al.  Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations , 1986, Proteins.

[153]  D. Wetlaufer.  Nucleation, rapid folding, and globular intrachain regions in proteins. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[154]  R. Abagyan,et al.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.

[155]  B. Berne,et al.  Smart walking: A new method for Boltzmann sampling of protein conformations , 1997 .

[156]  Shoji Takada,et al.  A Reversible Fragment Assembly Method for De Novo Protein Structure Prediction , 2003 .

[157]  Lydia E. Kavraki,et al.  Probabilistic roadmaps for path planning in high-dimensional configuration spaces , 1996, IEEE Trans. Robotics Autom..

[158]  J. Onuchic,et al.  Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.

[159]  David G. Luenberger,et al.  Linear and nonlinear programming , 1984 .

[160]  Thierry Siméon,et al.  Geometric algorithms for the conformational analysis of long protein loops , 2004, J. Comput. Chem..

[161]  F. Stillinger,et al.  Packing Structures and Transitions in Liquids and Solids , 1984, Science.

[162]  Ronald M Levy,et al.  Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. , 2003, Protein engineering.

[163]  L. Kay,et al.  The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase , 2004, Protein science : a publication of the Protein Society.

[164]  P. Wolynes,et al.  Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides , 1999, Proteins.

[165]  J. Garnier,et al.  Modeling of protein loops by simulated annealing , 1993, Protein science : a publication of the Protein Society.

[166]  Cecilia Clementi,et al.  Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.

[167]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[168]  Jun Yuan,et al.  A cyclic antimicrobial peptide produced in primate leukocytes by the ligation of two truncated alpha-defensins. , 1999, Science.

[169]  Chih-Cheng Chen,et al.  A combined optimization method for solving the inverse kinematics problems of mechanical manipulators , 1991, IEEE Trans. Robotics Autom..

[170]  A. Gronenborn,et al.  Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR. , 2004, Journal of molecular biology.

[171]  C DeLisi,et al.  Multiple copy sampling in protein loop modeling: Computational efficiency and sensitivity to dihedral angle perturbations , 1994, Protein science : a publication of the Protein Society.

[172]  Peter G Wolynes,et al.  Protein Structure Prediction:  The Next Generation. , 2006, Journal of chemical theory and computation.

[173]  Dinesh Manocha,et al.  Conformational analysis of molecular chains using nano-kinematics , 1995, Comput. Appl. Biosci..

[174]  Wilfred F van Gunsteren,et al.  Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. , 2006, The Journal of chemical physics.

[175]  H. Scheraga,et al.  Pattern recognition in the prediction of protein structure. I. Tripeptide conformational probabilities calculated from the amino acid sequence , 1989 .

[176]  Lee,et al.  New Monte Carlo algorithm: Entropic sampling. , 1993, Physical review letters.

[177]  Ron Goldman,et al.  Improving conformational searches by geometric screening , 2005, Bioinform..

[178]  Stu Borman,et al.  PROTEIN STRUCTURE WED TO DYNAMICS: Technique determines structure and motions of native proteins simultaneously , 2005 .

[179]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[180]  E. Shakhnovich,et al.  What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis. , 2000, Journal of molecular biology.

[181]  L. Kavraki,et al.  On the characterization of protein native state ensembles. , 2007, Biophysical journal.

[182]  Thierry Siméon,et al.  A random loop generator for planning the motions of closed kinematic chains using PRM methods , 2002, Proceedings 2002 IEEE International Conference on Robotics and Automation (Cat. No.02CH37292).

[183]  J. Onuchic,et al.  Prediction of folding mechanism for circular-permuted proteins. , 2001, Journal of molecular biology.

[184]  T. A. Jones,et al.  Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.

[185]  S. Grzesiek,et al.  Measurement of homo- and heteronuclear J couplings from quantitative J correlation. , 1994, Methods in enzymology.

[186]  Edward Lyman,et al.  Resolution exchange simulation. , 2005, Physical review letters.

[187]  J. Burdick.  On the inverse kinematics of redundant manipulators: characterization of the self-motion manifolds , 1989 .

[188]  M. Gruebele.  Protein folding: the free energy surface. , 2002, Current opinion in structural biology.

[189]  Matej Praprotnik,et al.  Adaptive resolution simulation of liquid water , 2007 .

[190]  A. Morgan,et al.  SOLVING THE 6R INVERSE POSITION PROBLEM USING A GENERIC-CASE SOLUTION METHODOLOGY , 1991 .

[191]  Lennart Nilsson,et al.  Advances in biomolecular simulations: methodology and recent applications , 2003, Quarterly Reviews of Biophysics.

[192]  Adrian A Canutescu,et al.  Cyclic coordinate descent: A robotics algorithm for protein loop closure , 2003, Protein science : a publication of the Protein Society.

[193]  K. Tai.  Conformational sampling for the impatient. , 2004, Biophysical chemistry.

[194]  A. Mathiowetz,et al.  De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology , 1995, Protein Science.

[195]  S. Englander,et al.  The loop problem in proteins: A monte carlo simulated annealing approach , 1993, Biopolymers.

[196]  H. Scheraga,et al.  Exact analytical loop closure in proteins using polynomial equations , 1999 .

[197]  Peter E Wright,et al.  Structure, dynamics, and catalytic function of dihydrofolate reductase. , 2004, Annual review of biophysics and biomolecular structure.

[198]  M. Karplus,et al.  PDB-based protein loop prediction: parameters for selection and methods for optimization. , 1997, Journal of molecular biology.

[199]  Adam Liwo,et al.  Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds. , 2004, Protein engineering, design & selection : PEDS.

[200]  John J. Craig,et al.  Introduction to Robotics Mechanics and Control , 1986 .

[201]  Charles L. Brooks,et al.  Identifying native‐like protein structures using physics‐based potentials , 2002, J. Comput. Chem..

[202]  M Karplus,et al.  Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations. , 1990, Journal of molecular biology.

[203]  Andrew E. Torda,et al.  Local elevation: A method for improving the searching properties of molecular dynamics simulation , 1994, J. Comput. Aided Mol. Des..

[204]  O. Olsen,et al.  Molecular dynamics simulations of protein-tyrosine phosphatase 1B. I. ligand-induced changes in the protein motions. , 1999, Biophysical journal.

[205]  M. Karplus,et al.  The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics , 1997 .

[206]  Itay Lotan,et al.  Real-space protein-model completion: an inverse-kinematics approach. , 2005, Acta crystallographica. Section D, Biological crystallography.

[207]  Vijay S Pande,et al.  Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. , 2004, The Journal of chemical physics.

[208]  L. Kay,et al.  NMR studies of protein structure and dynamics. , 2005, Journal of magnetic resonance.

[209]  Leonidas J. Guibas,et al.  Inverse Kinematics in Biology: The Protein Loop Closure Problem , 2005, Int. J. Robotics Res..

[210]  Juan C. Meza,et al.  OPT++: An object-oriented class library for nonlinear optimization , 1994 .

[211]  J. Skolnick,et al.  Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding , 2002, Proteins.

[212]  Rafael Brüschweiler,et al.  Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[213]  Ulrich H E Hansmann,et al.  Efficient sampling of protein structures by model hopping. , 2005, Physical review letters.

[214]  Cecilia Clementi,et al.  Unfolding the fold of cyclic cysteine‐rich peptides , 2008, Protein science : a publication of the Protein Society.

[215]  K. Fidelis,et al.  Comparison of systematic search and database methods for constructing segments of protein structure. , 1994, Protein engineering.

[216]  William F. DeGrado,et al.  How calmodulin binds its targets: sequence independent recognition of amphiphilic α-helices , 1990 .

[217]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[218]  Lydia E Kavraki,et al.  Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction , 2006, Proc. Natl. Acad. Sci. USA.

[219]  Gregory S. Chirikjian,et al.  General methods for computing hyper-redundant manipulator inverse kinematics , 1993, Proceedings of 1993 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS '93).

[220]  N. Niimura,et al.  Neutron protein crystallography: beyond the folding structure of biological macromolecules. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[221]  M. Quik,et al.  Vulnerability of 125I-α-Conotoxin MII Binding Sites to Nigrostriatal Damage in Monkey , 2001, The Journal of Neuroscience.

[222]  Lydia E. Kavraki,et al.  A randomized kinematics‐based approach to pharmacophore‐constrained conformational search and database screening , 2000 .

[223]  Nancy M. Amato,et al.  A kinematics-based probabilistic roadmap method for high DOF closed chain systems , 2004, IEEE International Conference on Robotics and Automation, 2004. Proceedings. ICRA '04. 2004.

[224]  J. Moult,et al.  An algorithm for determining the conformation of polypeptide segments in proteins by systematic search , 1986, Proteins.

[225]  N. Go,et al.  Ring Closure and Local Conformational Deformations of Chain Molecules , 1970 .

[226]  Lydia E. Kavraki,et al.  Finding Solutions of the Inverse Kinematics Problems in Computer-aided Drug Design , 2002 .

[227]  Alan M. Ferrenberg,et al.  New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.

[228]  T. Oas,et al.  The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[229]  P. R. Bevington,et al.  Data Reduction and Error Analysis for the Physical Sciences , 1969 .

[230]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[231]  L. Björck,et al.  Solution structure of the albumin-binding GA module: a versatile bacterial protein domain. , 1997, Journal of molecular biology.

[232]  D. Wigley,et al.  The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab. , 1994, Journal of molecular biology.

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

[234]  Joelle N Pelletier,et al.  Protein motions promote catalysis. , 2004, Chemistry & biology.

[235]  Richard S. Judson,et al.  Analysis of the genetic algorithm method of molecular conformation determination , 1993, J. Comput. Chem..