A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

Immune Literacy: Reading, Writing, and Editing Adaptive Immunity

(2020) Lucia Csepregi et al.   iScience

Biophysicochemical motifs in T cell receptor sequences distinguish repertoires from tumor-infiltrating lymphocytes and adjacent healthy tissue

(2019) Jared Ostmeyer et al.   CANCER RESEARCH

Structure-based methods for binding mode and binding affinity prediction for peptide-MHC complexes

(2019) Dinler A. Antunes et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Commonality despite exceptional diversity in the baseline human antibody repertoire

(2019) Bryan Briney et al.   NATURE

Scale-free networks are rare

(2019) Anna D. Broido et al.   Nature Communications

Five computational developability guidelines for therapeutic antibody profiling

(2019) Matthew I. J. Raybould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition

(2019) Philip Bradley et al.   Annual Review of Immunology

Sequence features of variable region determining physicochemical properties and polyreactivity of therapeutic antibodies

(2019) Maxime Lecerf et al.   MOLECULAR IMMUNOLOGY

Benchmark datasets of immune receptor-epitope structural complexes

(2019) Swapnil Mahajan et al.   BMC BIOINFORMATICS

Computational approaches to therapeutic antibody design: established methods and emerging trends

(2019) Richard A Norman et al.   BRIEFINGS IN BIOINFORMATICS

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

(2018) Edgar Liberis et al.   BIOINFORMATICS

ALLO: A tool to discriminate and prioritize allosteric pockets

(2018) Rahmad Akbar et al.   Chemical Biology & Drug Design

Antigen recognition by single-domain antibodies: structural latitudes and constraints

(2018) Kevin A. Henry et al.   mAbs

Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring

(2018) Esteban Lanzarotti et al.   MOLECULAR IMMUNOLOGY

TCRmodel: high resolution modeling of T cell receptors from sequence

(2018) Ragul Gowthaman et al.   NUCLEIC ACIDS RESEARCH

AbDb: antibody structure database—a database of PDB-derived antibody structures

(2018) Saba Ferdous et al.   Database-The Journal of Biological Databases and Curation

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design

(2018) Lance M. Hellman et al.   MOLECULAR THERAPY

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics

(2018) Timothy P. Riley et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition

(2018) Gwo-Yu Chuang et al.   STRUCTURE

Computational Design of Epitope-Specific Functional Antibodies

(2018) Guy Nimrod et al.   Cell Reports

Understanding the Significance and Implications of Antibody Numbering and Antigen-Binding Surface/Residue Definition

(2018) Mathieu Dondelinger et al.   Frontiers in Immunology

Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires

(2017) Victor Greiff et al.   JOURNAL OF IMMUNOLOGY

Local and global anatomy of antibody-protein antigen recognition

(2017) Meryl Wang et al.   JOURNAL OF MOLECULAR RECOGNITION

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Biophysical properties of the clinical-stage antibody landscape

(2017) Tushar Jain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles for computational design of binding antibodies

(2017) Dror Baran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass

(2017) Juan Salamanca Viloria et al.   Scientific Reports

Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development

(2017) Victor Greiff et al.   Cell Reports

Structure-based cross-docking analysis of antibody–antigen interactions

(2017) Krishna Praneeth Kilambi et al.   Scientific Reports

Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking

(2016) Daisuke Kuroda et al.   BIOINFORMATICS

ENRI: A tool for selecting structure-based virtual screening target conformations

(2016) Rahmad Akbar et al.   Chemical Biology & Drug Design

Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint

(2016) Brian D. Weitzner et al.   JOURNAL OF IMMUNOLOGY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

(2016) Duncan K. Ralph et al.   PLoS Computational Biology

Progress and challenges in predicting protein interfaces

(2015) Reyhaneh Esmaielbeiki et al.   BRIEFINGS IN BIOINFORMATICS

Inferring processes underlying B-cell repertoire diversity

(2015) Yuval Elhanati et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A hybrid method for protein-protein interface prediction

(2015) Howook Hwang et al.   PROTEIN SCIENCE

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Automated Identification of Complementarity Determining Regions (CDRs) Reveals Peculiar Characteristics of CDRs and B Cell Epitopes

(2014) Y. Ofran et al.   JOURNAL OF IMMUNOLOGY

Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition

(2014) Marc H. V. Van Regenmortel   JOURNAL OF MOLECULAR RECOGNITION

The therapeutic monoclonal antibody market

(2014) Dawn M Ecker et al.   mAbs

Origins of specificity and affinity in antibody–protein interactions

(2014) Hung-Pin Peng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cation-π, amino-π, π-π, and H-bond interactions stabilize antigen-antibody interfaces

(2014) Georgios A. Dalkas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational Identification of Antigen-Binding Antibody Fragments

(2013) A. Burkovitz et al.   JOURNAL OF IMMUNOLOGY

Antibody and Antigen Contact Residues Define Epitope and Paratope Size and Structure

(2013) J. W. Stave et al.   JOURNAL OF IMMUNOLOGY

bNAber: database of broadly neutralizing HIV antibodies

(2013) Alexey M. Eroshkin et al.   NUCLEIC ACIDS RESEARCH

The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops

(2013) Vered Kunik et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking

(2013) K. Krawczyk et al.   PROTEIN ENGINEERING DESIGN & SELECTION

The Structural Basis of Antibody-Antigen Recognition

(2013) Inbal Sela-Culang et al.   Frontiers in Immunology

Antigen–antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures

(2012) Thiruvarangan Ramaraj et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Predicting protein-protein interface residues using local surface structural similarity

(2012) Rafael A Jordan et al.   BMC BIOINFORMATICS

Antigen-binding site anatomy and somatic mutations in antibodies that recognize different types of antigens

(2012) Gopalan Raghunathan et al.   JOURNAL OF MOLECULAR RECOGNITION

An analysis of B-cell epitope discontinuity

(2012) Ganesh N. Sivalingam et al.   MOLECULAR IMMUNOLOGY

Structural analysis of B-cell epitopes in antibody:protein complexes

(2012) Jens Vindahl Kringelum et al.   MOLECULAR IMMUNOLOGY

Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure

(2012) Vered Kunik et al.   NUCLEIC ACIDS RESEARCH

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

(2012) Jens Vindahl Kringelum et al.   PLoS Computational Biology

Structural Consensus among Antibodies Defines the Antigen Binding Site

(2012) Vered Kunik et al.   PLoS Computational Biology

(φ,ψ)2 Motifs: A Purely Conformation-Based Fine-Grained Enumeration of Protein Parts at the Two-Residue Level

(2011) Scott A. Hollingsworth et al.   JOURNAL OF MOLECULAR BIOLOGY

Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data

(2011) Shandar Ahmad et al.   PLoS One

Extending Half-life by Indirect Targeting of the Neonatal Fc Receptor (FcRn) Using a Minimal Albumin Binding Domain

(2010) Jan Terje Andersen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

i-Patch: Interprotein contact prediction using local network information

(2010) Rebecca Hamer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Power-Law Distributions in Empirical Data

(2009) Aaron Clauset et al.   SIAM REVIEW

Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains

(2008) K.R. Abhinandan et al.   MOLECULAR IMMUNOLOGY

Toward high-resolution homology modeling of antibody Fvregions and application to antibody-antigen docking

(2008) Arvind Sivasubramanian et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS