ArticleJournal of chemical information and modeling2016
Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.
Article in Journal of chemical information and modeling, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- In Silico Design of a Trans-Amplifying RNA-Based Vaccine against SARS-CoV-2 Structural Proteins.Advances in virology · 2024Article
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- In silico protein function prediction: the rise of machine learning-based approaches.Medical review (2021) · 2023Review
- Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1.Acta crystallographica. Section F, Structural biology communications · 2023Article
- Tp0684, Tp0750, and Tp0792 Recombinant Proteins as Antigens for the Serodiagnosis of Syphilis.Indian journal of microbiology · 2022Article
- Structure-Activity Relationship of the Dimeric and Oligomeric Forms of a Cytotoxic Biotherapeutic Based on Diphtheria Toxin.Biomolecules · 2022Article
- Differences in Charge Distribution inInternational journal of molecular sciences · 2022Article
- Molecular characterization of linker and loop-mediated structural modulation and hinge motion in the C4-C5 domains of cMyBPC.Journal of structural biology · 2022Article
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- Common synaptic phenotypes arising from diverse mutations in the human NMDA receptor subunit GluN2A.Communications biology · 2022Article
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- Structural investigation of human cystine/glutamate antiporter system xFrontiers in molecular biosciences · 2022Article
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1 author.
Funding
Abstract
A method for the local refinement of protein structures that targets improvements in local stereochemistry while preserving the overall fold is presented. The method uses force field-based minimization and sampling via molecular dynamics simulations with a modified force field to bring bonds, angles, and torsion angles into an acceptable range for high-resolution protein structures. The method is implemented in the locPREFMD web server and was tested on computational models submitted to CASP11. Using MolProbity scores as the main assessment criterion, the locPREFMD method significantly improves the stereochemical quality of given input models close to the quality expected for experimental structures while maintaining the Cα coordinates of the initial model.
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