OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.
暂无分享,去创建一个
[1] J Moult,et al. Comparison of database potentials and molecular mechanics force fields. , 1997, Current opinion in structural biology.
[2] Yong Duan,et al. Comparison between Generalized-Born and Poisson–Boltzmann methods in physics-based scoring functions for protein structure prediction , 2005, Journal of molecular modeling.
[3] Arnab Mukherjee,et al. Orientation-dependent potential of mean force for protein folding. , 2005, The Journal of chemical physics.
[4] Teresa Head-Gordon,et al. Hydrophobic potential of mean force as a solvation function for protein structure prediction. , 2007, Structure.
[5] R Samudrala,et al. Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction , 2000, Protein science : a publication of the Protein Society.
[6] G. Klebe,et al. Statistical potentials and scoring functions applied to protein-ligand binding. , 2001, Current opinion in structural biology.
[7] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[8] 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.
[9] Hongyi Zhou,et al. What is a desirable statistical energy functions for proteins and how can it be obtained? , 2007, Cell Biochemistry and Biophysics.
[10] A. Sali,et al. Comparative protein structure modeling by iterative alignment, model building and model assessment. , 2003, Nucleic Acids Research.
[11] Xiaolong Wang,et al. Novel knowledge-based mean force potential at the profile level , 2006, BMC Bioinformatics.
[12] Christodoulos A. Floudas,et al. A novel high resolution CαCα distance dependent force field based on a high quality decoy set , 2006 .
[13] D Thirumalai,et al. Development of novel statistical potentials for protein fold recognition. , 2004, Current opinion in structural biology.
[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] James E Fitzgerald,et al. Reduced Cβ statistical potentials can outperform all‐atom potentials in decoy identification , 2007, Protein science : a publication of the Protein Society.
[16] Richard Bonneau,et al. An improved protein decoy set for testing energy functions for protein structure prediction , 2003, 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] David E. Kim,et al. Free modeling with Rosetta in CASP6 , 2005, Proteins.
[19] David Baker,et al. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. , 2004, Journal of molecular biology.
[20] Jie Liang,et al. Empirical potential function for simplified protein models: Combining contact and local sequence–structure descriptors , 2006, Proteins.
[21] Jianpeng Ma,et al. OPUS‐Ca: A knowledge‐based potential function requiring only Cα positions , 2007, Protein science : a publication of the Protein Society.
[22] Ram Samudrala,et al. A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence , 1999, Pacific Symposium on Biocomputing.
[23] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[24] D. Baker,et al. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.
[25] R. Jernigan,et al. Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.
[26] Hongyi Zhou,et al. An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state , 2004, Protein science : a publication of the Protein Society.
[27] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[28] 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.
[29] 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.
[30] D Gilis,et al. Protein Decoy Sets for Evaluating Energy Functions , 2004, Journal of biomolecular structure & dynamics.
[31] M. Levitt,et al. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. , 1996, Journal of molecular biology.
[32] 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.
[33] Rama Ranganathan,et al. Knowledge-based potential functions in protein design. , 2002, Current opinion in structural biology.
[34] 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.
[35] R Samudrala,et al. Ab initio construction of protein tertiary structures using a hierarchical approach. , 2000, Journal of molecular biology.
[36] R. Elber,et al. Distance‐dependent, pair potential for protein folding: Results from linear optimization , 2000, Proteins.
[37] D Gilis,et al. A new generation of statistical potentials for proteins. , 2006, Biophysical journal.
[38] Andrej Sali,et al. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. , 2006, Journal of molecular biology.
[39] M. Karplus,et al. Effective energy functions for protein structure prediction. , 2000, Current opinion in structural biology.
[40] 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.
[41] Rama Ranganathan,et al. Knowledge-based potentials in protein design. , 2006, Current opinion in structural biology.
[42] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[43] 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.
[44] J. Skolnick. In quest of an empirical potential for protein structure prediction. , 2006, Current opinion in structural biology.
[45] 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.