ArticleNature2024
Predicting multiple conformations via sequence clustering and AlphaFold2.
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Article in Nature, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 266 papers.
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266citing papers in PubMed
72.3field-weighted citation impact, top 1% of its field
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Who cites it
266 citing papers in PubMed, 470 citations in OpenAlex.
- 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
- Several multiple sequence alignment-perturbing methods enhance AlphaFold3 sampling of alternative protein states.Communications chemistry · 2026Article
- The Flexible Peripheral Segments Modulate the Catalytic Activity of the FAD-Containing Monooxygenase EthA fromBiomolecules · 2026Article
- Biasing Conformational Sampling in AlphaFold 3 and Boltz-2 via Pair Representation Scaling.Journal of chemical information and modeling · 2026Article
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- A curated benchmark for cofolding models on kinase conformational states.npj drug discovery · 2026Article
- Explainable AI reveals the allosteric blind spot in protein-ligand binding predictions.Cell reports. Physical science · 2026Article
- ESMDynamic: Fast and accurate prediction of protein dynamic contact maps from single sequences.Nature communications · 2026Article
- Article
- AFM-Fold: Rapid reconstruction of protein conformations from AFM images.Biophysical journal · 2026Article
- Synthetic sequence alignments as programmable probes of learned conformational landscapes in deep learning protein structure predictors.Bioinformatics (Oxford, England) · 2026Article
- β-Elemene Rescues Radiation-Induced Enteritis by Orchestrating a Host-Microbiome Circuit That Fuels Epigenetic DNA Repair.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- PETIMOT: a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks.Acta crystallographica. Section D, Structural biology · 2026Article
- AlphaFold reveals but sometimes distorts an organizational principle of protein folding.bioRxiv : the preprint server for biology · 2026Article
- Artificial Intelligence and Protein Design: A retrospective study on 20-year emerging trends and core research areas from bibliometric perspectives.Probiotics and antimicrobial proteins · 2026Article
- Structural Prediction and Functional Mechanistic Characterization of Farnesyl Diphosphate Synthase fromACS omega · 2026Article
- Benchmarking AI Protein Structure Predictors Reveals a Persistent Bias in Multi-State Proteins.bioRxiv : the preprint server for biology · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Where next for structural bioinformatics?PLoS biology · 2026Article
206 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 4 institutions in 2 countries.
Hannah K Wayment-Steele *Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
Adedolapo Ojoawo *Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.ORCID 0000-0003-3961-8935
Renee OttenDepartment of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.ORCID 0000-0001-7342-6131
Julia M ApitzDepartment of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.ORCID 0000-0002-9704-9729
Warintra PitsawongDepartment of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
Marc HömbergerDepartment of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.ORCID 0000-0003-2515-1094
Sergey OvchinnikovCenter for Systems Biology, Harvard University, Cambridge, MA, USA.ORCID 0000-0003-2774-2744
Lucy ColwellGoogle Research, Cambridge, MA, USA.ORCID 0000-0003-3148-0337
Dorothee KernDepartment of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA. dkern@brandeis.edu.ORCID 0000-0002-7631-8328
Howard Hughes Medical Institute · USBrandeis University · USGoogle (United States) · USHarvard University · US
Funding
TRD3 NMRbox: Bayesian AnalyticsP41GM111135 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI HOCH, JEFFREY C · 2015 to 2024
$14.0MNMR User Program at NMRFAMR24GM141526 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Katherine Anne Henzler-Wildman · 2021 to 2026
$6.4MMacromolecular Structure, Dynamics, and MechanismT32GM135126 · NIGMS · BRANDEIS UNIVERSITY · PI JEFF GELLES, Douglas Lowell Theobald · 2020 to 2026
$2.1MNIGMS NIH HHS P41 GM111135NIGMS NIH HHS R24 GM141526NIGMS NIH HHS T32 GM135126
Abstract
AlphaFold2 (ref.
Indexed as
Cluster AnalysisMachine LearningProtein ConformationProtein FoldingProteinsSequence AlignmentAntigens, BacterialBacterial ProteinsMutationRhodobacter sphaeroidesAntigens, BacterialBacterial Proteinsmpt53 protein, Mycobacterium tuberculosisProteins
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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.