NDLI: TRain: T-cell receptor automated immunoinformatics

Content Provider	Springer Nature : BioMed Central
Author	Seamann, Austin Bennett-Boehm, Maia Ehrlich, Ryan Gil, Anna Selin, Liisa Ghersi, Dario
Abstract	Background The scarcity of available structural data makes characterizing the binding of T-cell receptors (TCRs) to peptide-Major Histocompatibility Complexes (pMHCs) very challenging. The recent surge in sequencing data makes TCRs an ideal target for protein structure modeling. Through these 3D models, researchers can potentially identify key motifs on the TCR’s binding regions. Furthermore, computational methods can be employed to pair a TCR structure with a pMHC, leading to predictions of docked TCRpMHC structures. However, going from sequence to predicted 3D TCRpMHC complexes requires a non-trivial amount of steps and specialized immunoinformatics expertise. Results We developed a Python tool named TRain (T-cell Receptor Automated ImmunoiNformatics) to streamline this process by: (1) converting single-cell sequencing data into full TCR amino acid sequences; (2) efficiently submitting TCR amino acid sequences to existing TCR-specific modeling pipelines; (3) pairing modeled TCR structures with existing crystal structures of pMHC complexes in a non-biased manner before docking; (3) automating the preparation and submission process of TCRs and pMHCs for docking using the RosettaDock tool; and (4) providing scripts to analyze the predicted TCRpMHC interface. We illustrate the basic functionality of TRain with a case study, while further information can be found in a dedicated manual. Conclusions We introduced an open-source tool that streamlines going from full TCR sequence information to predicted 3D TCRpMHC complexes, using well-established tools. Analyzing these predicted complexes can provide deeper insights into the binding properties of TCRs, and can help shed light on one of the key steps in adaptive immune responses.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06074-8.pdf
Ending Page	11
Page Count	11
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-025-06074-8
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	26
Language	English
Publisher	BioMed Central
Publisher Date	2025-03-06
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms TCR modeling protein docking Immunoinformatics Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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