Another look at the conditions for the extraction of protein knowledge‐based potentials
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[1] G. Crippen,et al. Contact potential that recognizes the correct folding of globular proteins. , 1992, Journal of molecular biology.
[2] A. Kolinski,et al. Derivation of protein‐specific pair potentials based on weak sequence fragment similarity , 2000, Proteins.
[3] J R Banavar,et al. Interaction potentials for protein folding , 1998, Proteins.
[4] M. Betancourt. Smoothing the landscapes of protein folding: Insights from a minimal model , 1998 .
[5] 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.
[6] J Moult,et al. Comparison of database potentials and molecular mechanics force fields. , 1997, Current opinion in structural biology.
[7] D Gilis,et al. Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power. , 1998, European journal of biochemistry.
[8] S. Bryant,et al. The frequency of ion‐pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions , 1991, Proteins.
[9] Manfred J. Sippl,et al. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures , 1993, J. Comput. Aided Mol. Des..
[10] Cecilia Clementi,et al. Determination of interaction potentials of amino acids from native protein structures: Tests on simple lattice models , 1999 .
[11] P. De Los Rios,et al. Effective interactions cannot replace solvent effects in a lattice model of proteins. , 2003, Physical review letters.
[12] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[13] N. Linial,et al. On the design and analysis of protein folding potentials , 2000, Proteins.
[14] J. Straub,et al. Orientational potentials extracted from protein structures improve native fold recognition , 2004, Protein science : a publication of the Protein Society.
[15] M. Levitt,et al. Improved protein structure selection using decoy-dependent discriminatory functions , 2004, BMC Structural Biology.
[16] Jian Qiu,et al. Atomically detailed potentials to recognize native and approximate protein structures , 2005, Proteins.
[17] Robert L Jernigan,et al. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? , 2005, The Journal of chemical physics.
[18] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[19] J. Skolnick,et al. A distance‐dependent atomic knowledge‐based potential for improved protein structure selection , 2001, Proteins.
[20] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[21] A. Ben-Naim. STATISTICAL POTENTIALS EXTRACTED FROM PROTEIN STRUCTURES : ARE THESE MEANINGFUL POTENTIALS? , 1997 .
[22] Yang Zhang,et al. Template‐based modeling and free modeling by I‐TASSER in CASP7 , 2007, Proteins.
[23] F. Melo,et al. Novel knowledge-based mean force potential at atomic level. , 1997, Journal of molecular biology.
[24] 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.
[25] R. Samudrala,et al. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.
[26] Federico Fogolari,et al. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps , 2003, BMC Bioinformatics.
[27] A. Maritan,et al. Maximum entropy approach for deducing amino Acid interactions in proteins. , 2008, Physical review letters.
[28] Seung Yup Lee,et al. Analysis of TASSER‐based CASP7 protein structure prediction results , 2007, Proteins.
[29] Christopher M. Summa,et al. An atomic environment potential for use in protein structure prediction. , 2005, Journal of molecular biology.
[30] T Schlick,et al. Lattice protein folding with two and four‐body statistical potentials , 2001, Proteins.
[31] D. Baker,et al. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.
[32] An optimal derivation of a potential for protein folding , 1999 .
[33] S H Kim,et al. Environment-dependent residue contact energies for proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[34] M. Levitt,et al. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. , 2003, Journal of molecular biology.
[35] A. Tropsha,et al. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. , 2001, Journal of molecular biology.
[36] Hongyi Zhou,et al. A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding , 2004, Proteins.
[37] Marcos R Betancourt. A reduced protein model with accurate native‐structure identification ability , 2003, Proteins.
[38] Andrzej Kloczkowski,et al. Four‐body contact potentials derived from two protein datasets to discriminate native structures from decoys , 2007, Proteins.
[39] R A Goldstein,et al. How to generate improved potentials for protein tertiary structure prediction: A lattice model study , 2000, Proteins.
[40] K Nishikawa,et al. Knowledge-based potential defined for a rotamer library to design protein sequences. , 2001, Protein engineering.
[41] A. Sali,et al. Statistical potentials for fold assessment , 2009 .
[42] Eugene I Shakhnovich,et al. Lessons from the design of a novel atomic potential for protein folding , 2005, Protein science : a publication of the Protein Society.
[43] A. Tropsha,et al. HIV‐1 protease function and structure studies with the simplicial neighborhood analysis of protein packing method , 2008, Proteins.
[44] A Rojnuckarin,et al. Knowledge‐based interaction potentials for proteins , 1999, Proteins.
[45] E I Shakhnovich,et al. Specific nucleus as the transition state for protein folding: evidence from the lattice model. , 1994, Biochemistry.
[46] R. Jernigan,et al. Self‐consistent estimation of inter‐residue protein contact energies based on an equilibrium mixture approximation of residues , 1999, Proteins.
[47] M Vendruscolo,et al. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? , 2000, Proteins.
[48] Jianpeng Ma,et al. OPUS‐Ca: A knowledge‐based potential function requiring only Cα positions , 2007, Protein science : a publication of the Protein Society.
[49] M. Karplus,et al. Effective energy functions for protein structure prediction. , 2000, Current opinion in structural biology.
[50] S. Wodak,et al. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. , 1991, Journal of molecular biology.
[51] S. Wodak,et al. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. , 1994, Journal of molecular biology.
[52] L Serrano,et al. Analysis of the effect of local interactions on protein stability. , 1996, Folding & design.
[53] 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.
[54] U Bastolla,et al. A statistical mechanical method to optimize energy functions for protein folding. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[55] Lars Malmström,et al. Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home , 2007, Proteins.
[56] D Thirumalai,et al. Development of novel statistical potentials for protein fold recognition. , 2004, Current opinion in structural biology.
[57] E I Shakhnovich,et al. Evolution-like selection of fast-folding model proteins. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[58] Y. Matsuo,et al. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. , 1993, Protein engineering.
[59] Marcos R Betancourt. Knowledge-based potential for the polypeptide backbone. , 2008, The journal of physical chemistry. B.
[60] Bala Krishnamoorthy,et al. BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm481 Structural bioinformatics Four-Body Scoring Function for Mutagenesis , 2007 .
[61] Marcos R. Betancourt,et al. Protein Sequence Design by Energy Landscaping , 2002 .
[62] R. Jernigan,et al. Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.
[63] P. Koehl,et al. Influence of protein structure databases on the predictive power of statistical pair potentials , 1998, Proteins.
[64] E S Huang,et al. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. , 1997, Journal of molecular biology.
[65] K. Dill,et al. Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.
[66] R. Broglia,et al. Deriving amino acid contact potentials from their frequencies of occurrence in proteins: a lattice model study , 2004 .
[67] G. Casari,et al. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. , 1990, Journal of molecular biology.
[68] E. Domany,et al. Pairwise contact potentials are unsuitable for protein folding , 1998 .
[69] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[70] Qiaojun Fang,et al. A consistent set of statistical potentials for quantifying local side‐chain and backbone interactions , 2005, Proteins.
[71] D Thirumalai,et al. Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. , 2004, Journal of molecular graphics & modelling.
[72] A. Finkelstein,et al. Why do protein architectures have boltzmann‐like statistics? , 1995, Proteins.
[73] L A Mirny,et al. How to derive a protein folding potential? A new approach to an old problem. , 1996, Journal of molecular biology.
[74] Flavio Seno,et al. Variational Approach to Protein Design and Extraction of Interaction Potentials , 1998, cond-mat/9804054.