ArticleStructural dynamics (Melville, N.Y.)2024
Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies.
Article in Structural dynamics (Melville, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Learning protein representations with conformational dynamics.Bioinformatics (Oxford, England) · 2026Article
- Generating Dynamic Structures Through Physics-Based Sampling of Predicted Inter-Residue Geometries.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Disentangling coevolutionary constraints for modeling protein conformational heterogeneity.Communications chemistry · 2026Article
- Special Issue "Structural Dynamics of Macromolecules".International journal of molecular sciences · 2026Article
- AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturbed Versions of AlphaFold.Journal of chemical information and modeling · 2026Article
- PDBe: enhanced structural data exploration to facilitate discovery.Nucleic acids research · 2026Article
- BioEmu: AI-Powered Revolution in Scalable Protein Dynamics Simulation.Journal of cellular and molecular medicine · 2025Article
- Functional Ingredients: From Molecule to Market-AI-Enabled Design, Bioavailability, Consumer Impact, and Clinical Evidence.Foods (Basel, Switzerland) · 2025Review
- SeaMoon: From protein language models to continuous structural heterogeneity.Structure (London, England : 1993) · 2025Article
- Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions.Nature communications · 2025Article
- Generation of protein dynamics by machine learning.Current opinion in structural biology · 2025Review
- LIGYSIS-web: a resource for the analysis of protein-ligand binding sites.Nucleic acids research · 2025Article
- Analysing protein complexes in plant science: insights and limitation with AlphaFold 3.Botanical studies · 2025Review
- Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules.Journal of visualized experiments : JoVE · 2025Article
- Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational Plasticity within Organelles, Cells, and Tissues.Journal of proteome research · 2025Article
- PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank.Protein science : a publication of the Protein Society · 2025Article
- Predicting the conformational flexibility of antibody and T cell receptor complementarity-determining regions.Nature machine intelligence · 2025Article
- Comparative evaluation of methods for the prediction of protein-ligand binding sites.Journal of cheminformatics · 2024Article
- Introduction to the Special Issue Tribute to Olga Kennard (1924-2023).Structural dynamics (Melville, N.Y.) · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, and ESMFold, static representations are typically produced, which fail to fully capture macromolecular motion. Here, we discuss the importance of integrating experimental structures with computational clustering to explore the conformational landscapes that manifest protein function. We describe the method developed by the Protein Data Bank in Europe - Knowledge Base to identify distinct conformational states, demonstrate the resource's primary use cases, through examples, and discuss the need for further efforts to annotate protein conformations with functional information. Such initiatives will be crucial in unlocking the potential of protein dynamics data, expediting drug discovery research, and deepening our understanding of macromolecular mechanisms.
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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 Socratic graph.