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A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jmr.2158openalex-snapshot
Antigen‐binding site anatomy and somatic mutations in antibodies that recognize different types of antigens
inferredcites →https://doi.org/10.1002/jmr.2394openalex-snapshot
Specificity, polyspecificity, and heterospecificity of antibody‐antigen recognition
inferredcites →https://doi.org/10.1002/jmr.815openalex-snapshot
Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools
inferredcites →https://doi.org/10.1002/pro.2744openalex-snapshot
A hybrid method for protein–protein interface prediction
inferredcites →https://doi.org/10.1002/prot.21248openalex-snapshot
Prediction‐based fingerprints of protein–protein interactions
inferredcites →https://doi.org/10.1002/prot.22309openalex-snapshot
Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking
inferredcites →https://doi.org/10.1002/prot.22792openalex-snapshot
i‐Patch: Interprotein contact prediction using local network information
inferredcites →https://doi.org/10.1002/prot.24527openalex-snapshot
Cation–π, amino–π, π–π, and H‐bond interactions stabilize antigen–antibody interfaces
inferredcites →https://doi.org/10.1006/jmbi.1993.1648openalex-snapshot
Shape Complementarity at Protein/Protein Interfaces
inferredcites →https://doi.org/10.1006/jmbi.1996.0548openalex-snapshot
Antibody-antigen Interactions: Contact Analysis and Binding Site Topography
inferredcites →https://doi.org/10.1007/978-1-4939-6406-2_17openalex-snapshot
In Silico Prediction of Linear B-Cell Epitopes on Proteins
inferredcites →https://doi.org/10.1016/0022-2836(87)90412-8openalex-snapshot
Canonical structures for the hypervariable regions of immunoglobulins
inferredcites →https://doi.org/10.1016/0022-2836(91)90617-fopenalex-snapshot
Structure, function and properties of antibody binding sites
inferredcites →https://doi.org/10.1016/0167-5699(92)90088-oopenalex-snapshot
Immunoglobulins did not arise in evolution to fight infection
inferredcites →https://doi.org/10.1016/j.celrep.2017.04.054openalex-snapshot
Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development
inferredcites →https://doi.org/10.1016/j.celrep.2018.10.081openalex-snapshot
Computational Design of Epitope-Specific Functional Antibodies
inferredcites →https://doi.org/10.1016/j.copbio.2018.01.006openalex-snapshot
Induction of broadly neutralizing antibodies in Germinal Centre simulations
inferredcites →https://doi.org/10.1016/j.jmb.2011.12.022openalex-snapshot
(φ,ψ)2 Motifs: A Purely Conformation-Based Fine-Grained Enumeration of Protein Parts at the Two-Residue Level
inferredcites →https://doi.org/10.1016/j.jmb.2014.08.013openalex-snapshot
Restricted Diversity of Antigen Binding Residues of Antibodies Revealed by Computational Alanine Scanning of 227 Antibody–Antigen Complexes
inferredcites →https://doi.org/10.1016/j.molimm.2007.10.016openalex-snapshot
Computational characterization of B-cell epitopes
inferredcites →https://doi.org/10.1016/j.molimm.2008.05.022openalex-snapshot
Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains
inferredcites →https://doi.org/10.1016/j.molimm.2012.03.030openalex-snapshot
An analysis of B-cell epitope discontinuity
inferredcites →https://doi.org/10.1016/j.molimm.2012.06.001openalex-snapshot
Structural analysis of B-cell epitopes in antibody:protein complexes
inferredcites →https://doi.org/10.1016/j.molimm.2017.12.019openalex-snapshot
Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring
inferredcites →https://doi.org/10.1016/j.molimm.2019.06.012openalex-snapshot
Sequence features of variable region determining physicochemical properties and polyreactivity of therapeutic antibodies
inferredcites →https://doi.org/10.1016/j.semcdb.2017.10.017openalex-snapshot
The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics
inferredcites →https://doi.org/10.1016/j.str.2018.10.007openalex-snapshot
Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition
inferredcites →https://doi.org/10.1016/j.ymthe.2018.12.010openalex-snapshot
Improving T Cell Receptor On-Target Specificity via Structure-Guided Design
inferredcites →https://doi.org/10.1016/s0022-2836(02)01222-6openalex-snapshot
Analysis of the Antigen Combining Site: Correlations Between Length and Sequence Composition of the Hypervariable Loops and the Nature of the Antigen
inferredcites →https://doi.org/10.1016/s1074-7613(00)00006-6openalex-snapshot
Diversity in the CDR3 Region of VH Is Sufficient for Most Antibody Specificities
inferredcites →https://doi.org/10.1017/s0033583500000135openalex-snapshot
Structural basis for the specificity of antibody–antigen reactions and structural mechanisms for the diversification of antigen-binding specificities
inferredcites →https://doi.org/10.1038/322747a0openalex-snapshot
Continuous and discontinuous protein antigenic determinants
inferredcites →https://doi.org/10.1038/nature22383openalex-snapshot
Quantifiable predictive features define epitope-specific T cell receptor repertoires
inferredcites →https://doi.org/10.1038/nature22976openalex-snapshot
Identifying specificity groups in the T cell receptor repertoire
inferredcites →https://doi.org/10.1038/ng.3822openalex-snapshot
Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire
inferredcites →https://doi.org/10.1038/nri1977openalex-snapshot
Structural determinants of T-cell receptor bias in immunity
inferredcites →https://doi.org/10.1038/s41586-019-0879-yopenalex-snapshot
Commonality despite exceptional diversity in the baseline human antibody repertoire
inferredcites →https://doi.org/10.1038/s41598-017-01498-6openalex-snapshot
An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
inferredcites →https://doi.org/10.1038/srep41926openalex-snapshot
Limb proportions show developmental plasticity in response to embryo movement
inferredcites →https://doi.org/10.1039/c9me00034hopenalex-snapshot
Antibody–antigen complex modelling in the era of immunoglobulin repertoire sequencing
inferredcites →https://doi.org/10.1039/c9me00071bopenalex-snapshot
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires
inferredcites →https://doi.org/10.1073/pnas.1401131111openalex-snapshot
Origins of specificity and affinity in antibody–protein interactions
inferredcites →https://doi.org/10.1073/pnas.1616408114openalex-snapshot
Biophysical properties of the clinical-stage antibody landscape
inferredcites →https://doi.org/10.1073/pnas.1707171114openalex-snapshot
Principles for computational design of binding antibodies
inferredcites →https://doi.org/10.1073/pnas.1810576116openalex-snapshot
Five computational developability guidelines for therapeutic antibody profiling
inferredcites →https://doi.org/10.1073/pnas.1906020116openalex-snapshot
Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination
inferredcites →https://doi.org/10.1073/pnas.69.9.2659openalex-snapshot
Localization of Antibody-Combining Sites within the Variable Portions of Heavy and Light Chains
inferredcites →https://doi.org/10.1074/jbc.m110.164848openalex-snapshot
Extending Half-life by Indirect Targeting of the Neonatal Fc Receptor (FcRn) Using a Minimal Albumin Binding Domain
inferredcites →https://doi.org/10.1080/19420862.2018.1489633openalex-snapshot
Antigen recognition by single-domain antibodies: structural latitudes and constraints
inferredcites →https://doi.org/10.1084/jem.132.2.211openalex-snapshot
AN ANALYSIS OF THE SEQUENCES OF THE VARIABLE REGIONS OF BENCE JONES PROTEINS AND MYELOMA LIGHT CHAINS AND THEIR IMPLICATIONS FOR ANTIBODY COMPLEMENTARITY
inferredcites →https://doi.org/10.1089/cmb.2018.0175openalex-snapshot
Attentive Cross-Modal Paratope Prediction
inferredcites →https://doi.org/10.1093/bib/bbv027openalex-snapshot
Progress and challenges in predicting protein interfaces
inferredcites →https://doi.org/10.1093/bib/bbz095openalex-snapshot
Computational approaches to therapeutic antibody design: established methods and emerging trends
inferredcites →https://doi.org/10.1093/bioinformatics/18.1.175openalex-snapshot
SACS—Self-maintaining database of antibody crystal structure information
inferredcites →https://doi.org/10.1093/bioinformatics/btaa158openalex-snapshot
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
inferredcites →https://doi.org/10.1093/bioinformatics/btaa263openalex-snapshot
Learning context-aware structural representations to predict antigen and antibody binding interfaces
inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot
Biopython: freely available Python tools for computational molecular biology and bioinformatics
inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot
circlize implements and enhances circular visualization in R
inferredcites →https://doi.org/10.1093/bioinformatics/btu523openalex-snapshot
Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
inferredcites →https://doi.org/10.1093/bioinformatics/btw197openalex-snapshot
Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking
inferredcites →https://doi.org/10.1093/bioinformatics/btw771openalex-snapshot
Feature selection using a one dimensional naïve Bayes’ classifier increases the accuracy of support vector machine classification of CDR3 repertoires
inferredcites →https://doi.org/10.1093/bioinformatics/btx389openalex-snapshot
The interfacial character of antibody paratopes: analysis of antibody–antigen structures
inferredcites →https://doi.org/10.1093/bioinformatics/btx585openalex-snapshot
IntPred: a structure-based predictor of protein–protein interaction sites
inferredcites →https://doi.org/10.1093/bioinformatics/bty305openalex-snapshot
Parapred: antibody paratope prediction using convolutional and recurrent neural networks
inferredcites →https://doi.org/10.1093/bioinformatics/btz895openalex-snapshot
Antibody complementarity determining region design using high-capacity machine learning
inferredcites →https://doi.org/10.1093/database/bay040openalex-snapshot
AbDb: antibody structure database—a database of PDB-derived antibody structures
inferredcites →https://doi.org/10.1093/nar/27.1.209openalex-snapshot
IMGT, the international ImMunoGeneTics database
inferredcites →https://doi.org/10.1093/nar/gks480openalex-snapshot
Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure
inferredcites →https://doi.org/10.1093/nar/gkt1083openalex-snapshot
bNAber: database of broadly neutralizing HIV antibodies
inferredcites →https://doi.org/10.1093/nar/gkt887openalex-snapshot
3did: a catalog of domain-based interactions of known three-dimensional structure
inferredcites →https://doi.org/10.1093/nar/gkw1099openalex-snapshot
UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gky432openalex-snapshot
TCRmodel: high resolution modeling of T cell receptors from sequence
inferredcites →https://doi.org/10.1093/nar/gky550openalex-snapshot
High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis
inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot
The Pfam protein families database in 2019
inferredcites →https://doi.org/10.1093/protein/gzt027openalex-snapshot
The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops
inferredcites →https://doi.org/10.1093/protein/gzt043openalex-snapshot
Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking
inferredcites →https://doi.org/10.1093/protein/gzy017openalex-snapshot
Analysis of nanobody paratopes reveals greater diversity than classical antibodies
inferredcites →https://doi.org/10.1096/fj.01-0953hypopenalex-snapshot
Natural recognition repertoire and the evolutionary emergence of the combinatorial immune system
inferredcites →https://doi.org/10.1101/519108openalex-snapshot
Repertoire-Based Diagnostics Using Statistical Biophysics
inferredcites →https://doi.org/10.1101/606202openalex-snapshot
Deciphering interaction fingerprints from protein molecular surfaces
inferredcites →https://doi.org/10.1101/617860openalex-snapshot
Deep learning enables therapeutic antibody optimization in mammalian cells by deciphering high-dimensional protein sequence space
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1110/ps.062405906openalex-snapshot
Prediction of residues in discontinuous B‐cell epitopes using protein 3D structures
inferredcites →https://doi.org/10.1111/cbdd.12900openalex-snapshot
ENRI: A tool for selecting structure‐based virtual screening target conformations
inferredcites →https://doi.org/10.1111/cbdd.13161openalex-snapshot
ALLO : A tool to discriminate and prioritize allosteric pockets
inferredcites →https://doi.org/10.1111/imr.12665openalex-snapshot
Predicting the spectrum of TCR repertoire sharing with a data‐driven model of recombination
inferredcites →https://doi.org/10.1126/science.1170020openalex-snapshot
High-Throughput Sequencing of the Zebrafish Antibody Repertoire
inferredcites →https://doi.org/10.1126/science.2410982openalex-snapshot
Intrinsic and Extrinsic Factors in Protein Antigenic Structure
inferredcites →https://doi.org/10.1137/070710111openalex-snapshot
Power-Law Distributions in Empirical Data
inferredcites →https://doi.org/10.1146/annurev-immunol-042718-041757openalex-snapshot
Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition
inferredcites →https://doi.org/10.1146/annurev.immunol.2.1.67openalex-snapshot
The Antigenic Structure of Proteins: A Reappraisal
inferredcites →https://doi.org/10.1155/2017/2680160openalex-snapshot
Fundamentals and Methods for T- and B-Cell Epitope Prediction
inferredcites →https://doi.org/10.1158/0008-5472.can-18-2292openalex-snapshot
Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue
inferredcites →https://doi.org/10.1371/journal.pcbi.1002388openalex-snapshot
Structural Consensus among Antibodies Defines the Antigen Binding Site
inferredcites →https://doi.org/10.1371/journal.pcbi.1007636openalex-snapshot
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
inferredcites →https://doi.org/10.18637/jss.v064.i02openalex-snapshot
Fitting Heavy Tailed Distributions: The poweRlaw Package
inferredcites →https://doi.org/10.18653/v1/d15-1166openalex-snapshot
Effective Approaches to Attention-based Neural Machine Translation
inferredcites →https://doi.org/10.2174/ctmc-15680266-615openalex-snapshot
Current Topics in Medicinal Chemistry
inferredcites →https://doi.org/10.2307/2531532openalex-snapshot
Estimating the Population Size for Capture-Recapture Data with Unequal Catchability
inferredcites →https://doi.org/10.3389/fimmu.2017.00430openalex-snapshot
Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization
inferredcites →https://doi.org/10.3389/fimmu.2018.00224openalex-snapshot
Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
inferredcites →https://doi.org/10.3389/fimmu.2018.01698openalex-snapshot
Structurally Mapping Antibody Repertoires
inferredcites →https://doi.org/10.3389/fimmu.2018.02278openalex-snapshot
Understanding the Significance and Implications of Antibody Numbering and Antigen-Binding Surface/Residue Definition
inferredcites →https://doi.org/10.3389/fimmu.2019.00298openalex-snapshot
Antibody Specific B-Cell Epitope Predictions: Leveraging Information From Antibody-Antigen Protein Complexes
inferredcites →https://doi.org/10.4049/jimmunol.1200757openalex-snapshot
Computational Identification of Antigen-Binding Antibody Fragments
inferredcites →https://doi.org/10.4049/jimmunol.1203198openalex-snapshot
Antibody and Antigen Contact Residues Define Epitope and Paratope Size and Structure
inferredcites →https://doi.org/10.4049/jimmunol.1601137openalex-snapshot
Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint
inferredcites →https://doi.org/10.4049/jimmunol.181.9.6230openalex-snapshot
Automated Identification of Complementarity Determining Regions (CDRs) Reveals Peculiar Characteristics of CDRs and B Cell Epitopes
inferredcites →https://doi.org/10.4161/19420862.2015.989042openalex-snapshot
The therapeutic monoclonal antibody market
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.crmeth.2022.100269openalex-snapshot
Reference-based comparison of adaptive immune receptor repertoires
inferred← citeshttps://doi.org/10.1038/s41541-023-00788-7openalex-snapshot
The dengue-specific immune response and antibody identification with machine learning
inferred← citeshttps://doi.org/10.1038/s42256-021-00413-zopenalex-snapshot
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
inferred← citeshttps://doi.org/10.1080/19420862.2020.1729683openalex-snapshot
Understanding the human antibody repertoire
inferred← citeshttps://doi.org/10.1093/bib/bbaa318openalex-snapshot
Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab660openalex-snapshot
DLAB: deep learning methods for structure-based virtual screening of antibodies
inferred← citeshttps://doi.org/10.1101/2020.04.12.038158openalex-snapshot
Modern Hopfield Networks and Attention for Immune Repertoire Classification
inferred← citeshttps://doi.org/10.1146/annurev-chembioeng-101420-125021openalex-snapshot
Applications of Machine and Deep Learning in Adaptive Immunity
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008391openalex-snapshot
Using B cell receptor lineage structures to predict affinity
inferred← citeshttps://doi.org/10.14302/issn.2692-1537.ijcv-20-3459openalex-snapshot
Presentation of Neutralizing Antibodies in Single- or Pooled-Convalescent Immune Plasma from Donors to Prevent the Current SARS-CoV-2 Pandemic
inferred← citeshttps://doi.org/10.47749/t/unicamp.2021.1260506openalex-snapshot
Aplicação de redes neurais recorrentes ao projeto de anticorpos a partir da sequência de aminoácidos de epítopos
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