ArticleStructure (London, England : 1993)2016
New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.
Article in Structure (London, England : 1993), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Predicting side chain conformations in folded proteins by AlphaFold: Perspective and challenges.Biophysical journal · 2025Article
- Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins.bioRxiv : the preprint server for biology · 2025Article
- Conformational Analysis of UniformlyMolecules (Basel, Switzerland) · 2025Article
- The Damietta Server: a comprehensive protein design toolkit.Nucleic acids research · 2024Article
- Malonyl-CoA is a conserved endogenous ATP-competitive mTORC1 inhibitor.Nature cell biology · 2023Article
- The design of functional proteins using tensorized energy calculations.Cell reports methods · 2023Article
- Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs.Journal of chemical information and modeling · 2023Article
- Building protein structure-specific rotamer libraries.Bioinformatics (Oxford, England) · 2023Article
- A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations.Protein science : a publication of the Protein Society · 2022Article
- Thin-Plate Superstructures of the Immunogenic 33-mer Gliadin Peptide.Chembiochem : a European journal of chemical biology · 2022Article
- The role of α-sheet structure in amyloidogenesis: characterization and implications.Open biology · 2022Review
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1.Nucleic acids research · 2022Article
- Conformational sampling of CMT-2D associated GlyRS mutations.Brain multiphysics · 2022Article
- ProMod3-A versatile homology modelling toolbox.PLoS computational biology · 2021Article
- Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions.Biophysical journal · 2020Article
- Deciphering collaborative sidechain motions in proteins during molecular dynamics simulations.Scientific reports · 2020Article
- Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
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4 authors.
Funding
Abstract
Most rotamer libraries are generated from subsets of the PDB and do not fully represent the conformational scope of protein side chains. Previous attempts to rectify this sparse coverage of conformational space have involved application of weighting and smoothing functions. We resolve these limitations by using physics-based molecular dynamics simulations to determine more accurate frequencies of rotameric states. This work forms part of our Dynameomics initiative and uses a set of 807 proteins selected to represent 97% of known autonomous protein folds, thereby eliminating the bias toward common topologies found within the PDB. Our Dynameomics derived rotamer libraries encompass 4.8 × 10(9) rotamers, sampled from at least 51,000 occurrences of each of 93,642 residues. Here, we provide a backbone-dependent rotamer library, based on secondary structure ϕ/ψ regions, and an update to our 2011 backbone-independent library that addresses the doubling of our dataset since its original publication.
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