ArticleBioinformatics (Oxford, England)2018
PREFMD: a web server for protein structure refinement via molecular dynamics simulations.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Design a multi-epitope vaccine candidate against Acinetobacter baumannii using advanced computational methods.AMB Express · 2025Article
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules.Journal of molecular biology · 2025Review
- Molecular dynamic simulations to assess the structural variability of ClpV fromFrontiers in bioinformatics · 2025Article
- Bioinformatics approach for structure modeling, vaccine design, and molecular docking of Brucella candidate proteins BvrR, OMP25, and OMP31.Scientific reports · 2024Article
- The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.Mini reviews in medicinal chemistry · 2024Review
- Article
- Elevated Expression of theCancers · 2021Article
- Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy.International journal of molecular sciences · 2021Article
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Bioluminescent Multi-Characteristic Opsin for Simultaneous Optical Stimulation and Continuous Monitoring of Cortical Activities.Frontiers in cellular neuroscience · 2021Article
- Computational Methods for the Elucidation of Protein Structure and Interactions.Methods in molecular biology (Clifton, N.J.) · 2021Review
- CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2020Article
- Comparative modelling studies of fruit bromelain using molecular dynamics simulation.Journal of molecular modeling · 2020Article
- High-accuracy protein structures by combining machine-learning with physics-based refinement.Proteins · 2020Article
- Ten quick tips for homology modeling of high-resolution protein 3D structures.PLoS computational biology · 2020Article
- Driven to near-experimental accuracy by refinement via molecular dynamics simulations.Proteins · 2019Article
- MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics.Nucleic acids research · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein.Molecules (Basel, Switzerland) · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Summary: Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. Availability and implementation: PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. Contact: feig@msu.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.