Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Journal of Structural and Functional Genomics

• Publication date

  2011-06-15

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1007/s10969-011-9113-3PMID 21674234PMCID PMC3227679
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Particle Swarm Optimization

  2019cited by this paper
• Multibody coarse‐grained potentials for native structure recognition and quality assessment of protein models

  2011influential reference
• Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models.

  2011cited by this paper
• Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.

  2010cited by this paper
• Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

  2010cited by this paper
• A distance‐dependent atomic knowledge‐based potential and force for discrimination of native structures from decoys

  2009cited by this paper
• Backbone flexibility in computational protein design.

  2009cited by this paper
• A guide to template based structure prediction.

  2009cited by this paper
• Computer-aided design of functional protein interactions.

  2009cited by this paper
• Protein structure prediction and model quality assessment.

  2009cited by this paper
• Quality assessment of protein structure models.

  2009cited by this paper
• Enzyme (re)design: lessons from natural evolution and computation.

  2009cited by this paper
• Convergence and combination of methods in protein-protein docking.

  2009cited by this paper
• Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

  2009cited by this paper
• Long-timescale molecular dynamics simulations of protein structure and function.

  2009cited by this paper
• FINDSITE: a combined evolution/structure-based approach to protein function prediction

  2009cited by this paper
• Contrasting disease and nondisease protein aggregation by molecular simulation.

  2008cited by this paper
• Predicting 3D structures of protein-protein complexes.

  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

  2008cited by this paper
• Computational methods for calculation of ligand-binding affinity.

  2008cited by this paper
• Recent progress and future directions in protein-protein docking.

  2008cited by this paper
• Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes.

  2008cited by this paper
• Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions.

  2008cited by this paper
• Conformational stability and folding mechanisms of dimeric proteins.

  2008cited by this paper
• Packing regularities in biological structures relate to their dynamics.

  2007cited by this paper
• Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

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

  2007influential reference
• Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

  2006cited by this paper
• The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models.

  2006cited by this paper
• Coarse-grained normal mode analysis in structural biology.

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

  2005cited by this paper
• Inferring ideal amino acid interaction forms from statistical protein contact potentials

  2005cited by this paper
• Protein Decoy Sets for Evaluating Energy Functions

  2004cited by this paper
• Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations

  2003cited by this paper
• Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction

  2002cited by this paper
• A normalized root‐mean‐spuare distance for comparing protein three‐dimensional structures

  2001cited by this paper
• A distance‐dependent atomic knowledge‐based potential for improved protein structure selection

  2001cited by this paper
• Anisotropy of fluctuation dynamics of proteins with an elastic network model.

  2001cited by this paper
• Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction

  2000cited by this paper
• A database of macromolecular motions.

  1998cited by this paper
• An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction.

  1998cited by this paper
• Short‐range conformational energies, secondary structure propensities, and recognition of correct sequence‐structure matches

  1997cited by this paper
• Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.

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

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

  1996cited by this paper
• Harmonic analysis of large systems. I. Methodology

  1995cited by this paper
• Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

  1990cited by this paper
• Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

  1985cited by this paper
• Identification of common molecular subsequences.

  1981cited by this paper
• Approximating the inverse of a matrix for use in iterative algorithms on vector processors

  1979cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper
• Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins.

  1976cited by this paper

• Advancing deep variant phenotyping of mitochondrial enzyme complexes for precision medicine in allogeneic hematopoietic stem-cell transplantation

  2025cites this paper
• Unusual hardness and string-like structures relaxation of metallic glass investigated by in-situ synchrotron radiation

  2024cites this paper
• Multiscale modelling of biopolymers

  2024cites this paper
• Navigating protein landscapes with a machine-learned transferable coarse-grained model

  2023cites this paper
• Computational Ways to Enhance Protein Inhibitor Design

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

  2021cites this paper
• Broad Concepts from Polymers Applied to Protein Data

  2020cites this paper
• Searching for the origin of protein conformational changes: Protein responses to specific forces in simulations

  2019cites this paper
• SeqStruct: A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence

  2018cites this paper
• Using evolutionary covariance to infer protein sequence-structure relationships

  2018cites this paper
• Knowledge-based entropies improve the identification of native protein structures

  2017cites this paper
• Knowledge-based approaches for understanding structure-dynamics-function relationship in proteins

  2016cites this paper
• Distributions of experimental protein structures on coarse-grained free energy landscapes.

  2015cites this paper
• Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method

  2014cites this paper
• All‐atom and coarse‐grained simulations of the forced unfolding pathways of the SNARE complex

  2014cites this paper
• Many-body effect in ion binding to RNA.

  2014cites this paper
• Combining coarse‐grained nonbonded and atomistic bonded interactions for protein modeling

  2013cites this paper
• Identification of functionally key residues in AMPA receptor with a thermodynamic method.

  2013cites this paper
• Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

  2012influential citation
• Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses.

  2012cites this paper
• Elastic network normal modes provide a basis for protein structure refinement.

  2012cites this paper
• Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein

  2012cites this paper
• Protein sequence-structure relationships

  2011cites this paper