Accurate Conformation Sampling via Protein Structural Diffusion
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Abstract
Accurate sampling of protein conformations is pivotal for advances in biology and medicine. Although there has been tremendous progress in protein structure prediction in recent years due to deep learning, models that can predict the different stable conformations of proteins with high accuracy and structural validity are still lacking. Here, we introduce UFConf, a cutting-edge approach designed for robust sampling of diverse protein conformations based solely on amino acid sequences. This method transforms AlphaFold2 into a diffusion model by implementing a conformation-based diffusion process and adapting the architecture to process diffused inputs effectively. To counteract the inherent conformational bias in the Protein Data Bank, we developed a novel hierarchical reweighting protocol based on structural clustering. Our evaluations demonstrate that UFConf outperforms existing methods in terms of successful sampling and structural validity. The comparisons with long-time molecular dynamics show that UFConf can overcome the energy barrier existing in molecular dynamics simulations and perform more efficient sampling. Furthermore, We showcase UFConf's utility in drug discovery through its application in neural protein-ligand docking. In a blind test, it accurately predicted a novel protein-ligand complex, underscoring its potential to impact real-world biological research. Additionally, we present other modes of sampling using UFConf, including partial sampling with fixed motif, Langevin dynamics, and structural interpolation.
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- Authors
- Fan, J., Li, Z., Alcaide, E., Ke, G., Huang, H., & E, W.
- Affiliations
- Peking University (CN)
- Universitat de Barcelona (ES)
- DP Technology
- School of Mathematical Sciences
- Corresponding author
- Ke, Guolin
- Huang, Huaqing
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2024-09-28
- Volume
- 64
- Issue
- 22
- Pages
- 8414-8426
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W4402939815
- Cited by
- 17
- References
- 12
- Citations by year
- 2026: 7 · 2025: 8 · 2024: 2
- FWCI
- 2.32
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Key Research and Development Program of China (2021YFA1401600)
- National Natural Science Foundation of China (12074006, 12474056)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- diffusion models, AlphaFold2, conformational bias, structural clustering, molecular dynamics sampling, protein-ligand docking, drug discovery, Langevin dynamics, protein structure prediction
- MeSH terms
- Diffusion, Ligands, Protein Conformation, Proteins, Databases, Protein, Drug Discovery, Molecular Dynamics Simulation, Molecular Docking Simulation
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