Repertoire Builder

High-throughput structural modeling for B-cell and T-cell receptors

Dear Repertoire Builder users,
Please refrain from submitting large numbers of jobs in a short period of time, as it will overwhelm our server. For the time being, we ask that you limit your runs to 10 per 24 hour period. If we find that this limit is being exceeded, we will disable use of Repertoire Builder for the user in question. We hope to have a more scalable implementation in place shortly.
Users who have tried to circumvent the policy above by creating multiple accounts have been blocked. Everyone else, please follow the simple rules, which will allow everyone to use Repertoire Builder freely.

Header lines are not required if only submitting one sequence/sequence pair.
Jobs are limited to 10,000 models.
Header lines for sequence pairs(including blacklists, punctuation, etc.) must be identical in order to match heavy/beta sequences and alpha/light sequences.
Output file names will be extracted before the first separator in each header.
Separators are |, : and whitespace such as spaces or tabs.
Output file name length is limited to 32 characters.
Output file names must not contain characters other than the following: a-z, A-Z, 0-9, and the special characters - and _
Output file names must be unique for each sequence/sequence pair.
Sequences must be amino-acid sequences with no gaps(-) and no ambiguous residues(B, O, U, X, Z).
PDB ID blacklists are extracted between (( and )) in the header line.
Example: >name ((1a4j,1dba,1f3d))

A) MSAs of templates for each chain (heavy, light) are prepared CDRs, framework and orientation
B) for CDRs, MSAs are binned by the loop length
C) Extension of template MSAs retains original template-template relationships
D) query-template alignments are ranked by the dot-product between a query-template feature vector and an MSA-specific weight vector
E) top-scoring templates are used to assemble a coherent model.
Citation: Schritt, et al.; Molecular Systems Design & Engineering; 2019

ImmuneScape: TCR-pMHC modeling from amino acid sequences
InterClone: Quantifying functional convergence of lymphocyte receptor repertoires
AbAdapt: Antibody-specific epitope prediction

This service is in beta at the moment, and so we ask for your patience and understanding for any problems that may occur. Please contact us with any bug reports or feedback you may have.