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References from Methods for sequence and structural analysis of B and T cell receptor repertoires. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
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The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires
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Deep generative models for T cell receptor protein sequences
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Revisiting antibody modeling assessment for CDR-H3 loop
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Second antibody modeling assessment (AMA-II)
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High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations
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Kotai Antibody Builder: automated high-resolution structural modeling of antibodies
10.1093/bioinformatics/btu510 · 2014 · External reference
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10.1093/nar/gkx334
10.1093/nar/gkx334 · External reference
MAFFT-DASH: integrated protein sequence and structural alignment
2019 · External reference
Adding unaligned sequences into an existing alignment using MAFFT and LAST
10.1093/bioinformatics/bts578 · 2012 · External reference
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Quantitative prediction of the landscape of T cell epitope immunogenicity in sequence space
10.3389/fimmu.2019.00827 · 2019 · External reference
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10.1093/bioinformatics/btu523
10.1093/bioinformatics/btu523 · External reference
T-cell receptor cognate target prediction based on paired alpha and beta chain sequence and structural CDR loop similarities
10.3389/fimmu.2019.02080 · 2019 · External reference
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10.1093/nar/gks480
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Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server
10.1093/bioinformatics/btt369 · 2013 · External reference
Parapred: antibody paratope prediction using convolutional and recurrent neural networks
10.1093/bioinformatics/bty305 · 2018 · External reference
Antibody interface prediction with 3D Zernike descriptors and SVM
10.1093/bioinformatics/bty918 · 2019 · External reference
Attentive cross-modal paratope prediction
10.1089/cmb.2018.0175 · 2019 · External reference
Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking
10.1093/protein/gzt043 · 2013 · External reference
Improved method for linear B-cell epitope prediction using antigen's primary sequence
10.1371/journal.pone.0062216 · 2013 · External reference
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence
10.1186/s12859-017-1528-9 · 2017 · External reference
10.1093/nar/gkx346
10.1093/nar/gkx346 · External reference
Novel overlapping subgraph clustering for the detection of antigen epitopes
10.1093/bioinformatics/bty051 · 2018 · External reference
10.3389/fimmu.2019.00298
10.3389/fimmu.2019.00298 · External reference
10.1093/bioinformatics/btu790
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Improving B-cell epitope prediction and its application to global antibody-antigen docking
10.1093/bioinformatics/btu190 · 2014 · External reference
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10.1016/j.jmb.2015.09.014
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10.1093/bioinformatics/btz642 · 2020 · External reference
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Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2
10.1016/j.jmb.2015.07.016 · 2015 · External reference
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10.1002/prot.25183 · 2017 · External reference
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2019 · External reference
Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study
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10.1016/j.molcel.2018.12.018 · External reference
Previously hidden dynamics at the TCR-peptide-MHC interface revealed
10.4049/jimmunol.1800315 · 2018 · External reference
Structural model of the mIgM B-cell receptor transmembrane domain from self-association molecular dynamics simulations
10.3389/fimmu.2018.02947 · 2018 · External reference
The trinity of COVID-19: immunity, inflammation and intervention
2020 · External reference
Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients' B cells
10.1016/j.cell.2020.05.025 · 2020 · External reference
ASAP – A webserver for immunoglobulin-sequencing analysis pipeline
10.3389/fimmu.2018.01686 · 2018 · External reference
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bcRep: R package for comprehensive analysis of B cell receptor repertoire data
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10.3389/fimmu.2019.02533 · 2019 · External reference
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pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring
10.1093/bioinformatics/btt262 · 2013 · External reference
10.1093/nar/gkx407
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10.1093/nar/gkq311
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A web interface for easy flexible protein-protein docking with ATTRACT
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2020 · External reference
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