Advantages of fine-grained side chain conformer libraries.

No abstract is available for this paper.

• Publication year

  2003

• Venue

  Protein Engineering

• Publication date

  2003-12-01

• Fields of study

  Biology, Medicine, Physics, Chemistry

• Identifiers
  DOI 10.1093/PROTEIN/GZG143PMID 14983076
• 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.

• Structure validation by Cα geometry: ϕ,ψ and Cβ deviation

  2003cited by this paper
• Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all‐atom statistical potential and the AMBER force field with the Generalized Born solvation model

  2003cited by this paper
• Discrete restraint‐based protein modeling and the Cα‐trace problem

  2003cited by this paper
• Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles

  2003cited by this paper
• Rotamer libraries in the 21st century.

  2002cited by this paper
• On the role of the crystal environment in determining protein side-chain conformations.

  2002cited by this paper
• Extending the accuracy limits of prediction for side-chain conformations.

  2001cited by this paper
• Ab initio protein structure prediction using physicochemical potentials and a simplified off‐lattice model

  2001cited by this paper
• Constructing side chains on near-native main chains for ab initio protein structure prediction.

  2000cited by this paper
• Modeling of loops in protein structures

  2000cited by this paper
• The penultimate rotamer library

  2000influential reference
• Improved modeling of side‐chains in proteins with rotamer‐based methods: A flexible rotamer model

  1999cited by this paper
• Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

  1999influential reference
• Packing of sidechains in low-resolution models for proteins.

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

  1998cited by this paper
• Bayesian statistical analysis of protein side‐chain rotamer preferences

  1997cited by this paper
• Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.

  1997cited by this paper
• Protein folding: the endgame.

  1997cited by this paper
• Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.

  1993cited by this paper
• Backbone-dependent rotamer library for proteins. Application to side-chain prediction.

  1993cited by this paper
• Estimation and use of protein backbone angle probabilities.

  1993cited by this paper
• Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement

  1991cited by this paper
• A new approach to the rapid determination of protein side chain conformations.

  1991cited by this paper
• Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.

  1987cited by this paper
• A simplified representation of protein conformations for rapid simulation of protein folding.

  1976cited by this paper

• Real-valued Prediction of Side-chain Dihedrals in Proteins With Relation-Shape Convolution

  2021cites this paper
• Computational reconstruction of atomistic protein structures from coarse-grained models

  2019cites this paper
• In silico approaches and tools for the prediction of drug metabolism and fate: A review

  2019cites this paper
• Bioinformatics and Drug Discovery

  2019cites this paper
• Ramachandran maps for side chains in globular proteins

  2019cites this paper
• Systematic analysis of the sequence-structure-function relationships of thiamine diphosphate-dependent enzymes

  2015cites this paper
• Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering

  2015cites this paper
• Computational modeling and design of protein and polymeric Nano-assemblies

  2015cites this paper
• Protein side‐chain modeling with a protein‐dependent optimized rotamer library

  2014cites this paper
• Backbone dependency further improves side chain prediction efficiency in the Energy‐based Conformer Library (bEBL)

  2014influential citation
• Assessment of protein side‐chain conformation prediction methods in different residue environments

  2014cites this paper
• Methods for library-scale computational protein design.

  2014cites this paper
• De Novo Computational Protein Design

  2013cites this paper
• Binding Pocket Optimization by Computational Protein Design

  2012cites this paper
• An energy‐based conformer library for side chain optimization: Improved prediction and adjustable sampling

  2012cites this paper
• Structural informatics, modeling, and design with an open‐source Molecular Software Library (MSL)

  2012cites this paper
• Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone

  2011cites this paper
• Mean Field Theory for Protein Side-chain Prediction: Improvements and Applications

  2011cites this paper
• Theoretical and computational protein design.

  2011cites this paper
• SDSL-ESR-based protein structure characterization

  2010cites this paper
• Improved prediction of protein side‐chain conformations with SCWRL4

  2009cites this paper
• Novel Algorithms for Computational Protein Design, with Applications to Enzyme Redesign and Small-Molecule Inhibitor Design

  2009cites this paper
• Development and Validation of Optimization Methods for the Design of Protein Sequences and Combinatorial Libraries

  2009cites this paper
• Rotamer Libraries For Molecular Modeling And Design Of Proteins

  2009cites this paper
• Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions.

  2009cites this paper
• Evaluating and optimizing computational protein design force fields using fixed composition-based negative design

  2008cites this paper
• Modeling the Conformation of Side Chains in Proteins: Approaches, Problems and Possible Developments

  2008cites this paper
• Modeling of flexible side chains for protein-ligand docking

  2008cites this paper
• Computational Protein Design Force Field Optimization: A Negative Design Approach

  2007influential citation
• IRECS: A new algorithm for the selection of most probable ensembles of side‐chain conformations in protein models

  2007cites this paper
• Receptor-Binding Sites

  2006cites this paper
• Optimized Evolutionary Strategies in Conformational Sampling

  2006cites this paper
• An overview of recent developments in GPCR modelling: methods and validation

  2006cites this paper
• Combinatorial methods for small-molecule placement in computational enzyme design

  2006cites this paper
• Crystallographic refinement by knowledge-based exploration of complex energy landscapes.

  2005influential citation
• Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography.

  2004cites this paper