ArticleJournal of chemical theory and computation2023
AlphaFold2-RAVE: From Sequence to Boltzmann Ranking.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
What it found
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Who cites it
67 citing papers in PubMed.
- The Advantages of AI for Computational Protein Studies and Looking Ahead at the Next Challenges: Single Structures Are Not Enough.Journal of molecular biology · 2026Review
- Enhanced Sampling of Protein Conformations in AlphaFold3 with Repulsive Bias in the Diffusion Generative Model.JACS Au · 2026Article
- ESMDynamic: Fast and accurate prediction of protein dynamic contact maps from single sequences.Nature communications · 2026Article
- AlphaFold reveals but sometimes distorts an organizational principle of protein folding.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking AI Protein Structure Predictors Reveals a Persistent Bias in Multi-State Proteins.bioRxiv : the preprint server for biology · 2026Article
- Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families.BioData mining · 2026Review
- MAHLER: Integrating Metadynamics and Inverse Folding to Predict Antibody-Antigen Kinetics.bioRxiv : the preprint server for biology · 2026Article
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- AI-based methods for simulating, sampling, and predicting protein ensembles.Current opinion in structural biology · 2026Review
- Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways.Journal of chemical theory and computation · 2026Article
- Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.bioRxiv : the preprint server for biology · 2026Article
- Free Energy Calculation Method Based on Enhanced Sampling of Diverse Protein Conformations Predicted by Artificial Intelligence.The journal of physical chemistry letters · 2026Article
- Assessing the Performance of BioEmu in Understanding Protein Dynamics.International journal of molecular sciences · 2026Article
- Modernizing biomolecular NMR: The POKY suite.The Journal of biological chemistry · 2026Review
- Decrypting cryptic pockets with physics-based simulations and artificial intelligence.Current opinion in structural biology · 2026Review
- AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturbed Versions of AlphaFold.Journal of chemical information and modeling · 2026Article
- Advanced Computational Methods in Protein Simulations: A Case Study of Enhanced Sampling Applied to Membrane Transporters.Advances in experimental medicine and biology · 2026Review
- Reinforced molecular dynamics: Physics-infused generative machine learning model simulates protein motion.PNAS nexus · 2026Article
- Unlocking the undruggable spliceosome: generative AI and structural dynamics in cancer therapy.Frontiers in cell and developmental biology · 2026Review
- Integrating generative AI and physical tests to strengthen claims about emergent phenomena.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
While AlphaFold2 is rapidly being adopted as a new standard in protein structure predictions, it is limited to single structures. This can be insufficient for the inherently dynamic world of biomolecules. In this Letter, we propose AlphaFold2-RAVE, an efficient protocol for obtaining Boltzmann-ranked ensembles from sequence. The method uses structural outputs from AlphaFold2 as initializations for artificial intelligence-augmented molecular dynamics. We release the method as an open-source code and demonstrate results on different proteins.
Identifiers
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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.