ArticleBMC bioinformatics2011
Stereochemical errors and their implications for molecular dynamics simulations.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
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- HLA-EpiCheck: novel approach for HLA B-cell epitope prediction using 3D-surface patch descriptors derived from molecular dynamic simulations.Bioinformatics advances · 2024Article
- ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins.Communications biology · 2023Article
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- Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding.Journal of biomolecular structure & dynamics · 2022Article
- ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome.Science advances · 2021Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe.Frontiers in microbiology · 2021Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Chiral Interface of Amyloid Beta (Aβ): Relevance to Protein Aging, Aggregation and Neurodegeneration.Symmetry · 2020Article
- Functional identification of aOpen biology · 2019Article
- Article
- Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming.The Journal of biological chemistry · 2019Article
- Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.Journal of structural biology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundBiological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations.
resultsHere we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules.
conclusionsUse of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.
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