A new generation of statistical potentials for proteins.

Keywords

Formalism (music), Computer science, Algorithm, Decoy, Chemistry

References

• Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.晃 川手, 良一 行形 — 1996
• What should the Z‐score of native protein structures be?Steve Baule — 1998
• Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power.José María Sánchez Ventura — 1998
• Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemesElena Mármol — 2008
• Statistical potentials for fold assessmentEzio Santagata, Davide Dalmazzo, Lucia Tsantilis — 2002
• Orientational potentials extracted from protein structures improve native fold recognition伸一 望月 — 2004
• Database-derived potentials dependent on protein size for in silico folding and design.Ali Arya, Nuket Nowlan, Nicholas Sauriol — 2004
• Conformation of polypeptides and proteins.G. N. Ramachandran, V. Sasisekharan — 1968
• Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions.Marianne Rooman, Jean-Pierre A. Kocher, Shoshana J. Wodak — 1991
• Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.Manfred J. Sippl — 1990
• Comparison of database potentials and molecular mechanics force fields.John Moult — 1997
• Knowledge-based potentials for proteins.Manfred J. Sippl — 1995
• PQS: a protein quaternary structure file server.K. Henrick — 1998
• Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.Eric J. Alm, David Baker — 1999
• A lattice model for protein structure prediction at low resolution.David A. Hinds, Michael Levitt — 1992
• Hydrophobicity of amino acid residues in globular proteins.George D. Rose, Ari Geselowitz, Glenn J. Lesser — 1985
• Knowledge-based potential functions in protein design.William P. Russ, Rama Ranganathan — 2002
• Influence of protein structure databases on the predictive power of statistical pair potentialsEmiko Furuichi, Patrice Koehl — 1998
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresWolfgang Kabsch, Christian Sander — 1983
• Potential energy functions.Thomas A. Halgren — 1995

Cited by

• Extending the PRIME Model for Protein Aggregation to All Twenty Amino AcidsMookyung Cheon, Iksoo Chang, Carol K. Hall — 2010
• Discrimination of near-native decoy structures using statistical potentialsR. Hindi — 2012
• Optimisation de potentiels statistiques pour un modèle d'évolution soumis à des contraintes structurales. (Optimization of statistical potentials for Structurally constrained phylogenetic models)C. Bonnard — 2010
• A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and DynamicsHujun Shen, Zhen Xia, Guohui Li — 2012
• Computational Protein Design with Ensembles, Flexibility and Mathematical Guarantees, and its Application to Drug Resistance Prediction, and Antibody DesignPablo Gainza Cirauqui — 2015
• Towards an accurate prediction of the thermal stability of homologous proteinsFabrizio Pucci, Marianne Rooman — 2016
• OPUS‐Ca: A knowledge‐based potential function requiring only Cα positionsYinghao Wu, Mingyang Lu, Mingzhi Chen — 2007
• Predicting the Impact of Missense Mutations on Protein–Protein Binding AffinityMinghui Li, Marharyta Petukh, Emil Alexov — 2014
• Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical PotentialsFabrizio Pucci, Marianne Rooman — 2014
• Protein Conformation Motion Modeling Using Sep-CMA-ESMaxim Buzdalov, Sergey Knyazev, Yuri B. Porozov — 2014
• Statistical energy potential: reduced representation of Dehouck–Gilis–Rooman function by selecting against decoy datasetsWenwei Lu, Ri‐Bo Huang, Yu-Tuo Wei — 2012
• Modelling Thermal Stability Changes Upon Mutations in Proteins with Artificial Neural NetworksBenjamin Folch, Marianne Rooman, Yves Dehouck — 2010
• Hydrophobic potential of mean force as a solvation function for protein structure prediction.Matthew S. Lin, Nicolas L. Fawzi, Teresa Head‐Gordon — 2007
• Computational design of protein-ligand interfaces: potential in therapeutic developmentAndrew Morin, Jens Meiler, Laura S. Mizoue — 2011
• Structure-based mutant stability predictions on proteins of unknown structure.Giulia Gonnelli, Marianne Rooman, Yves Dehouck — 2012
• Statistical potential for assessment and prediction of protein structuresMin‐Yi Shen, Andrej Šali — 2006
• Perspective: Coarse-grained models for biomolecular systems.W. G. Noid — 2013
• Neural networks to predict protein stability changes upon mutationA. Grosfils, Yves Dehouck, Dimitri Gilis — 2008
• PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimalityYves Dehouck, Jean Marc Kwasigroch, Dimitri Gilis — 2011
• Protein Design Using Continuous RotamersPablo Gaínza, Kyle E. Roberts, Bruce R. Donald — 2012

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