Statistical Contact Potentials in Protein Coarse-Grained Modeling: From Pair to Multi-body Potentials

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Unknown venue

• Publication date

  Unknown publication date

• Fields of study

  Biology, Chemistry, Computer Science

• Identifiers
  DOI 10.1007/978-1-4419-6889-0_6
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

  2010cited by this paper
• Disordered, quasicrystalline and crystalline phases of densely packed tetrahedra

  2009cited by this paper
• Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

  2008cited by this paper
• Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

  2008influential reference
• Benchmarking consensus model quality assessment for protein fold recognition

  2007cited by this paper
• OPUS‐Ca: A knowledge‐based potential function requiring only Cα positions

  2007cited by this paper
• Four‐body contact potentials derived from two protein datasets to discriminate native structures from decoys

  2007cited by this paper
• Computational Methods for Protein Structure Prediction and Modeling

  2007cited by this paper
• A new generation of statistical potentials for proteins.

  2006cited by this paper
• Chapter 4: Knowledge-based energy functions for computational studies of proteins

  2006cited by this paper
• In quest of an empirical potential for protein structure prediction.

  2006cited by this paper
• New-generation amber united-atom force field.

  2006cited by this paper
• Empirical potential function for simplified protein models: Combining contact and local sequence–structure descriptors

  2006cited by this paper
• Novel knowledge-based mean force potential at the profile level

  2006cited by this paper
• Statistical potential for assessment and prediction of protein structures

  2006cited by this paper
• Inferring ideal amino acid interaction forms from statistical protein contact potentials

  2005cited by this paper
• Geometric cooperativity and anticooperativity of three‐body interactions in native proteins

  2005cited by this paper
• High-resolution protein folding with a transferable potential.

  2005cited by this paper
• A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes.

  2005cited by this paper
• Folding of small helical proteins assisted by small-angle X-ray scattering profiles.

  2005cited by this paper
• Atomically detailed potentials to recognize native and approximate protein structures

  2005cited by this paper
• Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures

  2005cited by this paper
• Determining protein topology from skeletons of secondary structures.

  2005cited by this paper
• Prediction of protein thermostability with a direction‐ and distance‐dependent knowledge‐based potential

  2005cited by this paper
• A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding

  2004cited by this paper
• Large‐scale prediction of protein geometry and stability changes for arbitrary single point mutations

  2004cited by this paper
• Computational Design of Combinatorial Peptide Library for Modulating Protein-Protein Interactions

  2004cited by this paper
• Developing optimal non-linear scoring function for protein design

  2004cited by this paper
• Computational Alanine Scanning of Protein-Protein Interfaces

  2004cited by this paper
• Protein Decoy Sets for Evaluating Energy Functions

  2004cited by this paper
• Protein modeling and structure prediction with a reduced representation.

  2004cited by this paper
• Simplicial edge representation of protein structures and alpha contact potential with confidence measure

  2003cited by this paper
• Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2).

  2003cited by this paper
• Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations

  2003cited by this paper
• Site-specific contributions to the pH dependence of protein stability

  2003cited by this paper
• Discrimination of native protein structures using atom–atom contact scoring

  2003cited by this paper
• The role of hydrophobic microenvironments in modulating pKa shifts in proteins

  2002cited by this paper
• Optimal potentials for predicting inter‐helical packing in transmembrane proteins

  2002cited by this paper
• Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction

  2002influential reference
• Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.

  2002cited by this paper
• Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.

  2002cited by this paper
• A simple physical model for binding energy hot spots in protein–protein complexes

  2002cited by this paper
• A distance‐dependent atomic knowledge‐based potential for improved protein structure selection

  2001influential reference
• Recent improvements in prediction of protein structure by global optimization of a potential energy function

  2001cited by this paper
• Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

  2001cited by this paper
• Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

  2001cited by this paper
• Disulfide recognition in an optimized threading potential.

  2000cited by this paper
• Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction

  2000cited by this paper
• Molecular simulation study of cooperativity in hydrophobic association

  2000cited by this paper
• Environment-dependent residue contact energies for proteins.

  2000cited by this paper
• Distance‐dependent, pair potential for protein folding: Results from linear optimization

  2000cited by this paper
• On the design and analysis of protein folding potentials

  2000cited by this paper
• Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

  2000cited by this paper
• Discrimination of near‐native protein structures from misfolded models by empirical free energy functions

  2000cited by this paper
• An empirical energy potential with a reference state for protein fold and sequence recognition

  1999cited by this paper
• Evaluation of short‐range interactions as secondary structure energies for protein fold and sequence recognition

  1999cited by this paper
• Self‐consistent estimation of inter‐residue protein contact energies based on an equilibrium mixture approximation of residues

  1999cited by this paper
• Designing potential energy functions for protein folding.

  1999cited by this paper
• A fast and simple method to calculate protonation states in proteins

  1999cited by this paper
• De novo protein design. I. In search of stability and specificity.

  1999cited by this paper
• Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins

  1999cited by this paper
• BLEEP—potential of mean force describing protein–ligand interactions: II. Calculation of binding energies and comparison with experimental data

  1999cited by this paper
• De novo protein design. II. Plasticity in sequence space.

  1999cited by this paper
• A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

  1999cited by this paper
• An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction.

  1998cited by this paper
• Pairwise contact potentials are unsuitable for protein folding

  1998cited by this paper
• Self-consistently optimized energy functions for protein structure prediction by molecular dynamics.

  1998cited by this paper
• United‐residue force field for off‐lattice protein‐structure simulations: III. Origin of backbone hydrogen‐bonding cooperativity in united‐residue potentials

  1998cited by this paper
• A united‐residue force field for off‐lattice protein‐structure simulations. II. Parameterization of short‐range interactions and determination of weights of energy terms by Z‐score optimization

  1997cited by this paper
• Statistical significance of hierarchical multi‐body potentials based on Delaunay tessellation and their application in sequence‐structure alignment

  1997cited by this paper
• VERIFY3D: assessment of protein models with three-dimensional profiles.

  1997cited by this paper
• Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence.

  1997cited by this paper
• Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

  1997cited by this paper
• Empirical potentials and functions for protein folding and binding.

  1997cited by this paper
• A new approach to protein fold recognition based on Delaunay tessellation of protein structure.

  1997cited by this paper
• Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

  1997cited by this paper
• Short‐range conformational energies, secondary structure propensities, and recognition of correct sequence‐structure matches

  1997cited by this paper
• A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data

  1997cited by this paper
• Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

  1996cited by this paper
• Emergence of Preferred Structures in a Simple Model of Protein Folding

  1996cited by this paper
• Structure-derived potentials and protein simulations.

  1996cited by this paper
• Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues

  1996cited by this paper
• SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence

  1996cited by this paper
• An iterative method for extracting energy-like quantities from protein structures.

  1996cited by this paper
• How to derive a protein folding potential? A new approach to an old problem.

  1996cited by this paper
• Statistical potentials extracted from protein structures: how accurate are they?

  1996cited by this paper
• Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials.

  1996cited by this paper
• Self‐consistently optimized statistical mechanical energy functions for sequence structure alignment

  1996cited by this paper
• Energy functions that discriminate X-ray and near native folds from well-constructed decoys.

  1996cited by this paper
• Why do protein architectures have boltzmann‐like statistics?

  1995cited by this paper
• Navigating the folding routes

  1995cited by this paper
• New algorithm for protein design.

  1995cited by this paper
• Protein folding potential functions

  1995cited by this paper
• Protein stability for single substitution mutants and the extent of local compactness in the denatured state.

  1994cited by this paper
• Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size

  1993cited by this paper
• Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures

  1993cited by this paper
• Engineering of stable and fast-folding sequences of model proteins.

  1993cited by this paper
• A new approach to protein fold recognition

  1992cited by this paper
• A lattice model for protein structure prediction at low resolution.

  1992cited by this paper
• Contact potential that recognizes the correct folding of globular proteins.

  1992influential reference

• New amino acid substitution matrix brings sequence alignments into agreement with structure matches

  2021cites this paper
• The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships

  2021cites this paper
• Multi-body effects in a coarse-grained protein force field.

  2021cites this paper
• SeqStruct: A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence

  2018cites this paper
• A computational model for controlling conformational cooperativity and function in proteins

  2018cites this paper
• Miyazawa-Jernigan Contact Potentials and Carter-Wolfenden Vapor-to-Cyclohexane and Water-to-Cyclohexane Scales as Parameters for Calculating Amino Acid Pair Distances

  2016cites this paper
• The Use of the Miyazawa-Jernigan Residue Contact Potential in Analyses of Molecular Interaction and Recognition with Complementary Peptides

  2016cites this paper
• DOCTEUR DE L'UNIVERSITÉ DE GRENOBLE

  2015cites this paper
• Nouvelles méthodes de calcul pour la prédiction des interactions protéine-protéine au niveau structural

  2015cites this paper
• Nouvelles méthodes de calcul pour la prédiction des interactions protéine-protéine au niveau structural. (Novel computational methods to predict protein-protein interactions on the structural level)

  2015cites this paper
• Knowledge of Native Protein-Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates

  2015cites this paper
• A Nonadaptive Origin of a Beneficial Trait: In Silico Selection for Free Energy of Folding Leads to the Neutral Emergence of Mutational Robustness in Single Domain Proteins

  2013cites this paper
• The Miyazawa-Jernigan Contact Energies Revisited

  2012cites this paper
• Protein sequence-structure relationships

  2011influential citation