AFsample: improving multimer prediction with AlphaFold using massive sampling
Abstract Summary The AlphaFold2 neural network model has revolutionized structural biology with unprecedented performance. We demonstrate that by stochastically perturbing the neural network by enabling dropout at inference combined with massive sampling, it is possible to improve the quality of the...
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| Published in: | Bioinformatics (Oxford, England) Vol. 39; no. 9 |
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| Main Author: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
Oxford University Press
02.09.2023
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| Subjects: | |
| ISSN: | 1367-4811, 1367-4803, 1367-4811 |
| Online Access: | Get full text |
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| Summary: | Abstract
Summary
The AlphaFold2 neural network model has revolutionized structural biology with unprecedented performance. We demonstrate that by stochastically perturbing the neural network by enabling dropout at inference combined with massive sampling, it is possible to improve the quality of the generated models. We generated ∼6000 models per target compared with 25 default for AlphaFold-Multimer, with v1 and v2 multimer network models, with and without templates, and increased the number of recycles within the network. The method was benchmarked in CASP15, and compared with AlphaFold-Multimer v2 it improved the average DockQ from 0.41 to 0.55 using identical input and was ranked at the very top in the protein assembly category when compared with all other groups participating in CASP15. The simplicity of the method should facilitate the adaptation by the field, and the method should be useful for anyone interested in modeling multimeric structures, alternate conformations, or flexible structures.
Availability and implementation
AFsample is available online at http://wallnerlab.org/AFsample. |
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| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1367-4811 1367-4803 1367-4811 |
| DOI: | 10.1093/bioinformatics/btad573 |