ArticleBioinformatics (Oxford, England)2014
Evol and ProDy for bridging protein sequence evolution and structural dynamics.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
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- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- InSty: A ProDy Module for Evaluating Protein Interactions and Stability.Journal of molecular biology · 2025Article
- Structural and thermodynamic impact of oncogenic mutations on the nucleosome core particle.Biophysical journal · 2025Article
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- Automated Engineering Protein Dynamics via Loop Grafting: ImprovingACS catalysis · 2025Article
- Computational electrostatic engineering of nanobodies for enhanced SARS-CoV-2 receptor binding domain recognition.Frontiers in molecular biosciences · 2025Article
- Dietary flavonoids form supramolecular assemblies, alter biochemistry, and enhance cell resilience.Frontiers in nutrition · 2025Article
- Alternating access of a bacterial homolog of neurotransmitter: sodium symporters determined from AlphaFold2 ensembles and DEER spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Structural shifts in TolC facilitate Efflux-Mediated β-lactam resistance.Communications biology · 2024Article
- Combining the Fragment Molecular Orbital and GRID Approaches for the Prediction of Ligand-Metalloenzyme Binding Affinity: The Case Study of hCA II Inhibitors.Molecules (Basel, Switzerland) · 2024Article
57 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
unlabelledCorrelations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. AVAILABILITY AND IMPLEMENTATION: ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/.
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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.