ArticleProteins2014
Assessment of protein side-chain conformation prediction methods in different residue environments.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Characterising Side Chain Conformations in Proteins UsingChemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- The design of functional proteins using tensorized energy calculations.Cell reports methods · 2023Article
- Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity.Frontiers in molecular biosciences · 2023Article
- Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol.Topics in current chemistry (Cham) · 2022Review
- Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol.Frontiers in immunology · 2022Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models.PloS one · 2020Article
- Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.PLoS computational biology · 2018Article
- Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.Proteins · 2018Article
- Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions.Protein engineering, design & selection : PEDS · 2017Article
- Modeling disordered protein interactions from biophysical principles.PLoS computational biology · 2017Article
- Quantifying side-chain conformational variations in protein structure.Scientific reports · 2016Article
- Protein structure prediction using residue- and fragment-environment potentials in CASP11.Proteins · 2016Article
- A three dimensional visualisation approach to protein heavy-atom structure reconstruction.BMC structural biology · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic-detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers.
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