ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes.
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.
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Tyler
T
Borrman
Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, 46556.
Jennifer
J
Cimons
Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, 46556.
Michael
M
Cosiano
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Michael
M
Purcaro
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850.
Brian G
BG
Pierce
Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, 46556.
Brian M
BM
Baker
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Zhiping
0000-0002-3032-7966
Z
Weng
D001665:Binding Sites; D016208:Databases, Factual; D015395:Histocompatibility Antigens Class I / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D006801:Humans; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D010455:Peptides / Q000737:chemistry* / Q000276:immunology; D011485:Protein Binding; D011487:Protein Conformation; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D012984:Software; D013816:Thermodynamics
D015395:Histocompatibility Antigens Class I; D008024:Ligands; D010455:Peptides; D011948:Receptors, Antigen, T-Cell
3D viewer; Rosetta; adaptive immunity; binding energy; protein modeling; scoring functions