.png){kind=icon}
返回
Improved multimer prediction using massive sampling with AlphaFold in CASP15
.png){kind=icon}
OA
AI
DOI：10.1002/prot.26562.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
AlphaFold2 has revolutionized structure prediction by achieving high accuracy comparable to experimentally determined structures. However, there is still room for improvement, especially for challenging cases like multimers. A key to the success of AlphaFold is its ability to assess and rank its own predictions. Our basic idea for the Wallner group in CASP15 was to exploit this excellent scoring function in AlphaFold by massive sampling. To achieve this goal, we conducted AlphaFold runs using six different settings, using templates, without templates, and with an increased number of recycles for both multimer v1 and v2 weights. In all instances, we enabled dropout layers during inference, allowing for sampling of uncertainty and enhancing the diversity of the generated models. In total, 274 289 models were generated for the 38 targets in CASP15, with a median of 4810 models per target. Of these 38 targets, 10 were high quality, 11 were medium quality, 11 were acceptable, and only 6 were incorrect. The improvement over the baseline method, NBIS-AF2-multimer, is substantial, with the mean DockQ increasing from 0.43 to 0.56, with several targets showing a DockQ score increase of +0.6 units. Remarkable, considering Wallner and NBIS-AF2-multimer were using identical input data. The success can be attributed to the diversified sampling using dropout with different settings and, in particular, the use of multimer v1, which is much more susceptible to sampling compared with v2. The method is available here: .
Keyword:
ensembles
interactions
machine learning
multimer
protein structure prediction
sampling
scoring
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
P
IF:
2.8
论文数:
6.6K
被引数:
1.4W
机构
引用论文
分享收藏Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology通过同源性模拟超出二元相互作用的同型和异型寡聚体的蛋白质四级结构.png)
SCIENTIFIC REPORTSOAAI
SCIENTIFIC REPORTSIF3.9
OAAI分享收藏Scoring function for automated assessment of protein structure template quality用于自动评估蛋白质结构模板质量的评分功能
PREAI
分享收藏Clustering huge protein sequence sets in linear time在线性时间内聚类巨大的蛋白质序列集NATURE COMMUNICATIONSOAAI
NATURE COMMUNICATIONSIF15.7
OAAI分享收藏Sampling alternative conformational states of transporters and receptors with AlphaFold2用AlphaFold2采样转运蛋白和受体的替代构象状态ELIFE
OAAI
ELIFEIF0
OAAI分享收藏The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNAMOLECULAR CELLOAAI
MOLECULAR CELLIF16.6
OAAI分享收藏US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexesUS-align: 蛋白质、核酸和大分子复合物的通用结构比对NATURE METHODSOAAI
NATURE METHODSIF32.1
OAAI分享收藏
查看更多内容