Borrman Tyler, Cimons Jennifer, Cosiano Michael, Purcaro Michael, Pierce Brian G, Baker Brian M, Weng Zhiping
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, 46556.
Proteins. 2017 May;85(5):908-916. doi: 10.1002/prot.25260. Epub 2017 Feb 16.
The ATLAS (Altered TCR Ligand Affinities and Structures) database (https://zlab.umassmed.edu/atlas/web/) is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest. We expect this database to facilitate the development of next-generation protein design algorithms targeting TCR-pMHC interactions. ATLAS can be easily parsed using modeling software that builds protein structures for training and testing. As an example, we provide structural models for all mutant TCRs in ATLAS, built using the Rosetta program. Utilizing these structures, we report a correlation of 0.63 between experimentally measured changes in binding energies and our predicted changes. Proteins 2017; 85:908-916. © 2016 Wiley Periodicals, Inc.
ATLAS（改变的TCR配体亲和力与结构）数据库（https://zlab.umassmed.edu/atlas/web/）是一个人工整理的知识库，包含野生型和突变型T细胞受体（TCR）及其抗原（主要组织相容性复合体呈递的肽，即pMHC）的结合亲和力。该数据库将实验测量的结合亲和力与TCR-pMHC复合物相应的三维（3D）结构相关联。用户可以浏览和搜索感兴趣的TCR、肽和MHC的亲和力、结构及实验细节。我们期望该数据库能促进针对TCR-pMHC相互作用的下一代蛋白质设计算法的开发。使用构建蛋白质结构用于训练和测试的建模软件可以轻松解析ATLAS。例如，我们提供了使用Rosetta程序构建的ATLAS中所有突变型TCR的结构模型。利用这些结构，我们报告了实验测量的结合能变化与我们预测的变化之间的相关性为0.63。《蛋白质》2017年；85:908 - 916。©2016威利期刊公司。
