Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding.
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B Jayaram | Aditya Mittal | Avinash Mishra | Satyanarayan Rao | B. Jayaram | A. Mittal | Avinash Mishra | Satyanarayan Rao
[1] Kyle A. Beauchamp,et al. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). , 2010, Journal of the American Chemical Society.
[2] U Bastolla,et al. How to guarantee optimal stability for most representative structures in the protein data bank , 2001, Proteins.
[3] R. Jernigan,et al. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.
[4] M. Levitt,et al. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. , 1996, Journal of molecular biology.
[5] Joseph A. Bank,et al. Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins , 2022 .
[6] E. Domany,et al. Pairwise contact potentials are unsuitable for protein folding , 1998 .
[7] Jie Liang,et al. Empirical potential function for simplified protein models: Combining contact and local sequence–structure descriptors , 2006, Proteins.
[8] Pascal Benkert,et al. QMEAN: A comprehensive scoring function for model quality assessment , 2008, Proteins.
[9] B Jayaram,et al. A Stoichiometry Driven Universal Spatial Organization of Backbones of Folded Proteins: Are there Chargaff's Rules for Protein Folding? , 2010, Journal of biomolecular structure & dynamics.
[10] K. Dill,et al. The Protein Folding Problem , 1993 .
[11] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[12] Taesung Park,et al. Response projected clustering for direct association with physiological and clinical response data , 2008, BMC Bioinformatics.
[13] P. K. Mehta,et al. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70% , 1995, Protein science : a publication of the Protein Society.
[14] Debashish Sahu,et al. Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins , 2006, Nucleic acids research.
[15] L. Pauling,et al. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[16] L A Mirny,et al. How to derive a protein folding potential? A new approach to an old problem. , 1996, Journal of molecular biology.
[17] J. Janin,et al. Surface and inside volumes in globular proteins , 1979, Nature.
[18] D. Case,et al. Dynamics of a type VI reverse turn in a linear peptide in aqueous solution. , 1997, Folding & design.
[19] M. Karplus,et al. Effective energy functions for protein structure prediction. , 2000, Current opinion in structural biology.
[20] M. Sternberg,et al. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.
[21] C Geourjon,et al. SOPM: a self-optimized method for protein secondary structure prediction. , 1994, Protein engineering.
[22] P M Cullis,et al. Affinities of amino acid side chains for solvent water. , 1981, Biochemistry.
[23] M Levitt,et al. A model of the molten globule state from molecular dynamics simulations. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[24] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[25] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[26] V. Lim. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. , 1974, Journal of molecular biology.
[27] A. Godzik,et al. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets , 1995, Protein science : a publication of the Protein Society.
[28] Andrzej Kloczkowski,et al. Four‐body contact potentials derived from two protein datasets to discriminate native structures from decoys , 2007, Proteins.
[29] John C. Wootton,et al. Non-globular Domains in Protein Sequences: Automated Segmentation Using Complexity Measures , 1994, Comput. Chem..
[30] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[31] Christian Cole,et al. The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..
[32] B. Lee,et al. The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.
[33] A Kolinski,et al. Correlation between knowledge‐based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper , 1999, Proteins.
[34] R. Doolittle,et al. A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.
[35] W. L. Jorgensen,et al. Molecular dynamics simulations of the unfolding of apomyoglobin in water. , 1993, Biochemistry.
[36] D J Osguthorpe,et al. Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor. , 1979, Journal of molecular biology.
[37] Pierre Baldi,et al. SCRATCH: a protein structure and structural feature prediction server , 2005, Nucleic Acids Res..
[38] Christophe G. Lambert,et al. ESyPred3D: Prediction of proteins 3D structures , 2002, Bioinform..
[39] M. Sternberg,et al. Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.
[40] K. Dill,et al. An iterative method for extracting energy-like quantities from protein structures. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[41] András Fiser,et al. Effects of amino acid composition, finite size of proteins, and sparse statistics on distance‐dependent statistical pair potentials , 2007, Proteins.
[42] 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.
[43] Pascal Benkert,et al. QMEAN server for protein model quality estimation , 2009, Nucleic Acids Res..
[44] D. Thirumalai,et al. Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes , 2008, Protein science : a publication of the Protein Society.
[45] K. Dill. Dominant forces in protein folding. , 1990, Biochemistry.
[46] V. Pande,et al. The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. , 2002, Journal of the American Chemical Society.
[47] Nidhi Arora,et al. Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments , 1998 .
[48] Jeffrey Skolnick,et al. M-TASSER: an algorithm for protein quaternary structure prediction. , 2008, Biophysical journal.
[49] David Baker,et al. Protein Structure Prediction Using Rosetta , 2004, Numerical Computer Methods, Part D.
[50] B. Rost,et al. Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.
[51] Yang Cao,et al. NCACO-score: An effective main-chain dependent scoring function for structure modeling , 2011, BMC Bioinformatics.
[52] A. Roitberg,et al. All-atom structure prediction and folding simulations of a stable protein. , 2002, Journal of the American Chemical Society.
[53] A. Fersht,et al. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[54] A. Kolinski,et al. Derivation of protein‐specific pair potentials based on weak sequence fragment similarity , 2000, Proteins.
[55] Qiaojun Fang,et al. Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm. , 2006, Journal of molecular biology.
[56] Nidhi Arora,et al. Strength of hydrogen bonds in helices , 1997, J. Comput. Chem..
[57] P. Wolynes,et al. The energy landscapes and motions of proteins. , 1991, Science.
[58] Solvation thermodynamics of amino acids Assessment of the electrostatic contribution and force-field dependence , 1997 .
[59] Leszek Rychlewski,et al. FFAS03: a server for profile–profile sequence alignments , 2005, Nucleic Acids Res..
[60] William L. Jorgensen,et al. Free energy calculations: a breakthrough for modeling organic chemistry in solution , 1989 .
[61] N. Linial,et al. On the design and analysis of protein folding potentials , 2000, Proteins.
[62] B Jayaram,et al. Backbones of folded proteins reveal novel invariant amino acid neighborhoods. , 2011, Journal of biomolecular structure & dynamics.
[63] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[64] M. Levitt,et al. Molecular dynamics of native protein. I. Computer simulation of trajectories. , 1983, Journal of molecular biology.
[65] Andrej ⩽ali,et al. Comparative protein modeling by satisfaction of spatial restraints , 1995 .
[66] Bhyravabhotla Jayaram,et al. Free Energy Analysis of the Conformational Preferences of A and B Forms of DNA in Solution , 1998 .
[67] H. Berendsen,et al. COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY , 1990 .
[68] M Levitt,et al. Molecular dynamics of native protein. II. Analysis and nature of motion. , 1983, Journal of molecular biology.
[69] Eric J. Sorin,et al. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. , 2001, Journal of molecular biology.
[70] A. Godzik,et al. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? , 1997, Protein science : a publication of the Protein Society.
[71] B. Jayaram,et al. Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding. , 2001, Journal of medicinal chemistry.
[72] Peter L. Freddolino,et al. Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. , 2008, Biophysical journal.
[73] David B. Searls,et al. Grand challenges in computational biology , 1998 .
[74] C. Brooks,et al. First-principles calculation of the folding free energy of a three-helix bundle protein. , 1995, Science.
[75] B Jayaram,et al. Protein Structure Evaluation using an All-Atom Energy Based Empirical Scoring Function , 2006, Journal of biomolecular structure & dynamics.
[76] A A Salamov,et al. Protein secondary structure prediction using local alignments. , 1997, Journal of molecular biology.
[77] B Jayaram,et al. A computational pathway for bracketing native-like structures fo small alpha helical globular proteins. , 2005, Physical chemistry chemical physics : PCCP.
[78] Eric J. Sorin,et al. β-hairpin folding simulations in atomistic detail using an implicit solvent model1 , 2001 .
[79] András Fiser,et al. New statistical potential for quality assessment of protein models and a survey of energy functions , 2010, BMC Bioinformatics.
[80] Bhyravabhotla Jayaram,et al. Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field , 1998 .
[81] Andrzej Kloczkowski,et al. GOR V server for protein secondary structure prediction , 2005, Bioinform..
[82] Bart De Moor,et al. Gene prioritization and clustering by multi-view text mining , 2010, BMC Bioinformatics.
[83] Wei Zhang,et al. SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model , 2008, PloS one.
[84] C Kooperberg,et al. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.
[85] R. Jernigan,et al. Self‐consistent estimation of inter‐residue protein contact energies based on an equilibrium mixture approximation of residues , 1999, Proteins.
[86] Adam Liwo,et al. Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes , 2001 .
[87] M. Sippl. Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.
[88] Bhyravabhotla Jayaram,et al. Local dielectric environment of B-DNA in solution : Results from a 14 ns molecular dynamics trajectory , 1998 .
[89] K. Dill,et al. From Levinthal to pathways to funnels , 1997, Nature Structural Biology.
[90] W. Kabsch,et al. How good are predictions of protein secondary structure? , 1983, FEBS letters.
[91] Adrien Treuille,et al. Predicting protein structures with a multiplayer online game , 2010, Nature.
[92] Ceslovas Venclovas,et al. Progress over the first decade of CASP experiments , 2005, Proteins.
[93] B. McConkey,et al. Discrimination of native protein structures using atom–atom contact scoring , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[94] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[95] Rahul Raman,et al. Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds , 2010, PloS one.
[96] Ceslovas Venclovas,et al. Assessment of progress over the CASP experiments , 2003, Proteins.
[97] M. Karplus,et al. Dynamics of folded proteins , 1977, Nature.
[98] L. Pauling,et al. The pleated sheet, a new layer configuration of polypeptide chains. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[99] M. Prueitt. Computer Simulation of Molecular Dynamics. , 1971 .
[100] P. Y. Chou,et al. Prediction of protein conformation. , 1974, Biochemistry.
[101] D. Beveridge,et al. Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.
[102] Jeffrey Skolnick,et al. Performance of the Pro‐sp3‐TASSER server in CASP8 , 2009, Proteins.
[103] David Baker,et al. Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..
[104] E. Shakhnovich,et al. Analysis of knowledge‐based protein‐ligand potentials using a self‐consistent method , 2008, Protein science : a publication of the Protein Society.
[105] Shing-Chung Ngan,et al. PROTINFO: new algorithms for enhanced protein structure predictions , 2005, Nucleic Acids Res..
[106] A. Li,et al. Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to x-ray crystallographic and NMR data. , 1995, Protein engineering.
[107] D. Baker,et al. Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins , 1999, Proteins.
[108] J. Skolnick,et al. A distance‐dependent atomic knowledge‐based potential for improved protein structure selection , 2001, Proteins.
[109] M J Sternberg,et al. Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM , 2001, Proteins.
[110] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[111] R L Jernigan,et al. Short‐range conformational energies, secondary structure propensities, and recognition of correct sequence‐structure matches , 1997, Proteins.
[112] R. Samudrala,et al. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.
[113] P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .
[114] P. Kollman,et al. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.
[115] R. Jernigan,et al. Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.
[116] Kengo Kinoshita,et al. PrDOS: prediction of disordered protein regions from amino acid sequence , 2007, Nucleic Acids Res..
[117] P. Flory. Principles of polymer chemistry , 1953 .
[118] D A Parry,et al. Quantitative comparison of the ability of hydropathy scales to recognize surface β‐strands in proteins , 2001, Proteins.
[119] Paul A. Bates,et al. Domain Fishing: a first step in protein comparative modelling , 2002, Bioinform..
[120] David T. Jones,et al. pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination , 2009, Bioinform..
[121] Peter L. Freddolino,et al. Force field bias in protein folding simulations. , 2009, Biophysical journal.
[122] Aviezri S. Fraenkel,et al. Complexity of protein folding , 1993 .
[123] A. Giuliani,et al. Bmc Structural Biology a Knowledge-based Structure-discriminating Function That Requires Only Main-chain Atom Coordinates , 2008 .
[124] Qiaojun Fang,et al. A consistent set of statistical potentials for quantifying local side‐chain and backbone interactions , 2005, Proteins.
[125] Pinak Chakrabarti,et al. Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins , 2009, BMC Structural Biology.
[126] X. Daura,et al. Reversible peptide folding in solution by molecular dynamics simulation. , 1998, Journal of molecular biology.
[127] W E Stites,et al. Packing is a key selection factor in the evolution of protein hydrophobic cores. , 2001, Biochemistry.
[128] J. Onuchic,et al. Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.
[129] Eugene I Shakhnovich,et al. Native atom types for knowledge-based potentials: application to binding energy prediction. , 2004, Journal of medicinal chemistry.
[130] Hongyi Zhou,et al. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction , 2002, Protein science : a publication of the Protein Society.
[131] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[132] David S. Goodsell,et al. The RCSB Protein Data Bank: redesigned web site and web services , 2010, Nucleic Acids Res..
[133] B Jayaram,et al. ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins , 2007, Journal of Biosciences.
[134] Jianpeng Ma,et al. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. , 2008, Journal of molecular biology.
[135] A. Sali,et al. Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.
[136] N. Guex,et al. SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.
[137] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[138] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[139] L. Pauling,et al. Atomic coordinates and structure factors for two helical configurations of polypeptide chains. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[140] Christophe Combet,et al. Geno3D: automatic comparative molecular modelling of protein , 2002, Bioinform..
[141] S Banu Ozkan,et al. The protein folding problem: when will it be solved? , 2007, Current opinion in structural biology.
[142] András Fiser,et al. Structural Characteristics of Novel Protein Folds , 2010, PLoS Comput. Biol..
[143] Nidhi Arora,et al. Strength of hydrogen bonds in α helices , 1997 .