Nessim Raouraoua, Marc F Lensink, Guillaume Brysbaert
{"title":"Massive Sampling Strategy for Antibody-Antigen Targets in CAPRI Round 55 With MassiveFold.","authors":"Nessim Raouraoua, Marc F Lensink, Guillaume Brysbaert","doi":"10.1002/prot.26802","DOIUrl":null,"url":null,"abstract":"<p><p>Massive sampling with AlphaFold2 improves protein-protein complex predictions. This has been shown during the last CASP15-CAPRI blind prediction round by the AFsample tool. However, more difficult targets including antibody-antigen binding remain challenging. CAPRI Round 55 consisted of three antibody-antigen targets and one heterotrimer. We used our AlphaFold2-based MassiveFold, running 6 prediction pools, each with their own set of parameters, to produce in total more than 6000 predictions per target. We show here that massive sampling categorically produces acceptable to high quality predictions, however it is clear that the AlphaFold2 confidence score cannot be used to identify the best models in the set. We also show that, contrary to what was done before for CASP15-CAPRI with AFsample, increasing the sampling without activating the dropout provides the best models for most of the targets of Round 55.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2000,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proteins-Structure Function and Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/prot.26802","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Massive sampling with AlphaFold2 improves protein-protein complex predictions. This has been shown during the last CASP15-CAPRI blind prediction round by the AFsample tool. However, more difficult targets including antibody-antigen binding remain challenging. CAPRI Round 55 consisted of three antibody-antigen targets and one heterotrimer. We used our AlphaFold2-based MassiveFold, running 6 prediction pools, each with their own set of parameters, to produce in total more than 6000 predictions per target. We show here that massive sampling categorically produces acceptable to high quality predictions, however it is clear that the AlphaFold2 confidence score cannot be used to identify the best models in the set. We also show that, contrary to what was done before for CASP15-CAPRI with AFsample, increasing the sampling without activating the dropout provides the best models for most of the targets of Round 55.
期刊介绍：
PROTEINS : Structure, Function, and Bioinformatics publishes original reports of significant experimental and analytic research in all areas of protein research: structure, function, computation, genetics, and design. The journal encourages reports that present new experimental or computational approaches for interpreting and understanding data from biophysical chemistry, structural studies of proteins and macromolecular assemblies, alterations of protein structure and function engineered through techniques of molecular biology and genetics, functional analyses under physiologic conditions, as well as the interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates. Research in protein and peptide biochemistry directed toward synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function, is also within the scope of PROTEINS. In addition to full-length reports, short communications (usually not more than 4 printed pages) and prediction reports are welcome. Reviews are typically by invitation; authors are encouraged to submit proposed topics for consideration.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
