Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies

Ab-Ligity: identifying sequence-dissimilar antibodies that bind to the same epitope

(2021) Wing Ki Wong et al.   mAbs

A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid antibodies

(2021) Eve Richardson et al.   mAbs

Machine Learning Applied to Determine the Molecular Descriptors Responsible for the Viscosity Behavior of Concentrated Therapeutic Antibodies

(2021) Pin-Kuang Lai et al.   MOLECULAR PHARMACEUTICS

Machine Learning for Biologics: Opportunities for Protein Engineering, Developability, and Formulation

(2021) Harini Narayanan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Antibody design using LSTM based deep generative model from phage display library for affinity maturation

(2021) Koichiro Saka et al.   Scientific Reports

Predicting Immunogenicity Risk in Biopharmaceuticals

(2021) Nikolet Doneva et al.   Symmetry-Basel

Low-N protein engineering with data-efficient deep learning

(2021) Surojit Biswas et al.   NATURE METHODS

Robustification of RosettaAntibody and Rosetta SnugDock

(2021) Jeliazko R. Jeliazkov et al.   PLoS One

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

(2021) Alexander Rives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues

(2021) Fan Yang et al.   SCIENCE

Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery

(2021) Andreas H. Laustsen et al.   TRENDS IN BIOTECHNOLOGY

Protein design and variant prediction using autoregressive generative models

(2021) Jung-Eun Shin et al.   Nature Communications

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

(2021) Rahmad Akbar et al.   Cell Reports

Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification

(2021) Daniel R. Ripoll et al.   PLoS Computational Biology

A single donor is sufficient to produce a highly functional in vitro antibody library

(2021) M. Frank Erasmus et al.   Communications Biology

AbsoluRATE: An in-silico method to predict the aggregation kinetics of native proteins

(2021) Puneet Rawat et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Humanization of antibodies using a machine learning approach on large-scale repertoire data

(2021) Claire Marks et al.   BIOINFORMATICS

A Brief History of De Novo Protein Design: Minimal, Rational, and Computational

(2021) Derek N. Woolfson   JOURNAL OF MOLECULAR BIOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Exploring the sequence features determining amyloidosis in human antibody light chains

(2021) Puneet Rawat et al.   Scientific Reports

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

(2021) Xianggen Liu et al.   PLoS Computational Biology

Germline-Dependent Antibody Paratope States and Pairing Specific VH-VL Interface Dynamics

(2021) Monica L. Fernández-Quintero et al.   Frontiers in Immunology

Immune2vec: Embedding B/T Cell Receptor Sequences in ℝN Using Natural Language Processing

(2021) Miri Ostrovsky-Berman et al.   Frontiers in Immunology

Machine learning prediction of methionine and tryptophan photooxidation susceptibility

(2021) Jared A. Delmar et al.   Molecular Therapy-Methods & Clinical Development

Structure-based protein design with deep learning

(2021) Sergey Ovchinnikov et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms

(2021) Mohammed AlQuraishi et al.   NATURE METHODS

CPAD 2.0: a repository of curated experimental data on aggregating proteins and peptides

(2020) Puneet Rawat et al.   AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design

(2020) Daisuke Kuroda et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Coarse-grained molecular dynamics simulations for understanding the impact of short-range anisotropic attractions on structure and viscosity of concentrated monoclonal antibody solutions

(2020) Amjad Chowdhury et al.   MOLECULAR PHARMACEUTICS

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

(2020) Gert-Jan Bekker et al.   Scientific Reports

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice

(2020) Aleksandr Kovaltsuk et al.   PLoS Computational Biology

Machine learning enabled autonomous microstructural characterization in 3D samples

(2020) Henry Chan et al.   npj Computational Materials

Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces

(2020) Srivamshi Pittala et al.   BIOINFORMATICS

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

(2020) Cédric R Weber et al.   BIOINFORMATICS

Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data

(2020) Birkir Reynisson et al.   JOURNAL OF PROTEOME RESEARCH

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

mmCSM-AB: guiding rational antibody engineering through multiple point mutations

(2020) Yoochan Myung et al.   NUCLEIC ACIDS RESEARCH

Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex

(2020) Dmitrii S. Shcherbinin et al.   PLoS Computational Biology

ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning

(2020) Xinmeng Li et al.   PLoS Computational Biology

Solubility-Weighted Index: fast and accurate prediction of protein solubility

(2020) Bikash K Bhandari et al.   BIOINFORMATICS

proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking

(2020) F Ambrosetti et al.   BIOINFORMATICS

Signal Peptides Generated by Attention-Based Neural Networks

(2020) Zachary Wu et al.   ACS Synthetic Biology

A single molecular descriptor to predict solution behavior of therapeutic antibodies

(2020) Jonathan S. Kingsbury et al.   Science Advances

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function

(2020) Amelia Villegas-Morcillo et al.   BIOINFORMATICS

CoV-AbDab: the Coronavirus Antibody Database

(2020) Matthew I J Raybould et al.   BIOINFORMATICS

Prediction of immunogenicity for humanized and full human therapeutic antibodies

(2020) Shide Liang et al.   PLoS One

Conditional out-of-distribution generation for unpaired data using transfer VAE

(2020) Mohammad Lotfollahi et al.   BIOINFORMATICS

Conformational Ensembles of Antibodies Determine Their Hydrophobicity

(2020) Franz Waibl et al.   BIOPHYSICAL JOURNAL

Top product forecasts for 2021

(2020) Lisa Urquhart   NATURE REVIEWS DRUG DISCOVERY

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

(2019) Zachary Sethna et al.   BIOINFORMATICS

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties

(2019) Monica L. Fernández-Quintero et al.   Frontiers in Immunology

Vitamin D Is Required for ILC3 Derived IL-22 and Protection From Citrobacter rodentium Infection

(2019) Yang-Ding Lin et al.   Frontiers in Immunology

Genesis of the αβ T-cell receptor

(2019) Thomas Dupic et al.   PLoS Computational Biology

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

(2019) Michael Schantz Klausen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Development of a high-throughput solubility screening assay for use in antibody discovery

(2019) Qing Chai et al.   mAbs

DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks

(2019) Mostafa Karimi et al.   BIOINFORMATICS

Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility

(2019) Aleksander Kuriata et al.   NUCLEIC ACIDS RESEARCH

Rapid global characterization of immunoglobulin G1 following oxidative stress

(2019) Yao Chen et al.   mAbs

Application of interpretable artificial neural networks to early monoclonal antibodies development

(2019) Lorenzo Gentiluomo et al.   EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS

Physicochemical Stability of Monoclonal Antibodies: A Review

(2019) Yoann Le Basle et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Insights into the IgG heavy chain engineering patent landscape as applied to IgG4 antibody development

(2019) Christophe Dumet et al.   mAbs

Thera-SAbDab: the Therapeutic Structural Antibody Database

(2019) Matthew I J Raybould et al.   NUCLEIC ACIDS RESEARCH

The ABCD database: a repository for chemically defined antibodies

(2019) Wanessa C Lima et al.   NUCLEIC ACIDS RESEARCH

Affinity Maturation Enhances Antibody Specificity but Compromises Conformational Stability

(2019) Laila Shehata et al.   Cell Reports

Antibody Complementarity Determining Region Design Using High-Capacity Machine Learning

(2019) Ge Liu et al.   BIOINFORMATICS

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

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

Anti-drug Antibodies Against Immune Checkpoint Blockers: Impairment of drug efficacy or indication of immune activation?

(2019) Diego Enrico et al.   CLINICAL CANCER RESEARCH

Boosting therapeutic potency of antibodies by taming Fc domain functions

(2019) Tae Hyun Kang et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Dissecting the molecular basis of high viscosity of monospecific and bispecific IgG antibodies

(2019) Cholpon Tilegenova et al.   mAbs

NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions

(2019) Bruno Alvarez et al.   MOLECULAR & CELLULAR PROTEOMICS

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

Modeling Antibody-Antigen Complexes by Information-Driven Docking

(2019) Francesco Ambrosetti et al.   STRUCTURE

cAb-Rep: A Database of Curated Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody Prevalence

(2019) Yicheng Guo et al.   Frontiers in Immunology

High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

(2019) Ian Setliff et al.   CELL

An Empirical Quantitative Model Describing Simultaneously Temperature and Concentration Effects on Protein Solution Viscosity

(2019) Walter Schwenger et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

(2019) P. Gainza et al.   NATURE METHODS

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

(2018) Edgar Liberis et al.   BIOINFORMATICS

DeepSol: a deep learning framework for sequence-based protein solubility prediction

(2018) Sameer Khurana et al.   BIOINFORMATICS

SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation

(2018) Justina Jankauskaitė et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Tutorial on Monoclonal Antibody Pharmacokinetics and its Considerations in Early Development

(2018) Meric Ovacik et al.   CTS-Clinical and Translational Science

iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories

(2018) Brian D. Corrie et al.   IMMUNOLOGICAL REVIEWS

Recurrent Neural Network Model for Constructive Peptide Design

(2018) Alex T. Müller et al.   Journal of Chemical Information and Modeling

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

A human endothelial cell-based recycling assay for screening of FcRn targeted molecules

(2018) Algirdas Grevys et al.   Nature Communications

High-throughput immune repertoire analysis with IGoR

(2018) Quentin Marcou et al.   Nature Communications

Molecular generative model based on conditional variational autoencoder for de novo molecular design

(2018) Jaechang Lim et al.   Journal of Cheminformatics

Animal models for evaluation of albumin-based therapeutics

(2018) Jeannette Nilsen et al.   Current Opinion in Chemical Engineering

Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding

(2018) Sara D’Angelo et al.   Frontiers in Immunology

Progress and Challenges in the Design and Clinical Development of Antibodies for Cancer Therapy

(2018) Juan C. Almagro et al.   Frontiers in Immunology

AbPredict 2: A server for accurate and unstrained structure prediction of antibody variable domains

(2018) Gideon Lapidoth et al.   BIOINFORMATICS

Towards a combinatorial approach for the prediction of immunoglobulin G half-life and clearance

(2018) Dennis R. Goulet et al.   DRUG METABOLISM AND DISPOSITION

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

(2018) Aleksandr Kovaltsuk et al.   JOURNAL OF IMMUNOLOGY

Humanization of Antibodies using a Statistical Inference Approach

(2018) Alejandro Clavero-Álvarez et al.   Scientific Reports

Antibody interface prediction with 3D Zernike descriptors and SVM

(2018) Sebastian Daberdaku et al.   BIOINFORMATICS

Structure, heterogeneity and developability assessment of therapeutic antibodies

(2018) Yingda Xu et al.   mAbs

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Thermal stability of single-domain antibodies estimated by molecular dynamics simulations

(2018) Gert-Jan Bekker et al.   PROTEIN SCIENCE

sdAb-DB: The Single Domain Antibody Database

(2018) Emily E. Wilton et al.   ACS Synthetic Biology

Computational Design of Epitope-Specific Functional Antibodies

(2018) Guy Nimrod et al.   Cell Reports

Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database

(2018) Swapnil Mahajan et al.   Frontiers in Immunology

Prediction and Reduction of the Aggregation of Monoclonal Antibodies

(2017) Rob van der Kant et al.   JOURNAL OF MOLECULAR BIOLOGY

abYsis: Integrated Antibody Sequence and Structure—Management, Analysis, and Prediction

(2017) Mark B. Swindells et al.   JOURNAL OF MOLECULAR BIOLOGY

In-silico prediction of concentration-dependent viscosity curves for monoclonal antibody solutions

(2017) Dheeraj S. Tomar et al.   mAbs

Changes in complementarity-determining regions significantly alter IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics

(2017) Nicole M. Piche-Nicholas et al.   mAbs

Public antibodies to malaria antigens generated by two LAIR1 insertion modalities

(2017) Kathrin Pieper et al.   NATURE

Modeling and docking of antibody structures with Rosetta

(2017) Brian D Weitzner et al.   Nature Protocols

Next generation antibody drugs: pursuit of the 'high-hanging fruit'

(2017) Paul J. Carter et al.   NATURE REVIEWS DRUG DISCOVERY

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

(2017) Saqib Mir et al.   NUCLEIC ACIDS RESEARCH

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

Alternative Splicing May Not Be the Key to Proteome Complexity

(2017) Michael L. Tress et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Immunoregulatory Roles of Antibody Glycosylation

(2017) Madeleine F. Jennewein et al.   TRENDS IN IMMUNOLOGY

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

(2017) Victor Greiff et al.   Cell Reports

Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation

(2017) Marek Wieczorek et al.   Frontiers in Immunology

Rapid and accurate in silico solubility screening of a monoclonal antibody library

(2017) Pietro Sormanni et al.   Scientific Reports

Variations in MHC Class II Antigen Processing and Presentation in Health and Disease

(2016) Emil R. Unanue et al.   Annual Review of Immunology

Immunoglobulin isotype knowledge and application to Fc engineering

(2016) Randall J Brezski et al.   CURRENT OPINION IN IMMUNOLOGY

Assessment of Solvated Interaction Energy Function for Ranking Antibody–Antigen Binding Affinities

(2016) Traian Sulea et al.   Journal of Chemical Information and Modeling

ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation

(2016) Jinwoo Leem et al.   mAbs

Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product development

(2016) Dheeraj S. Tomar et al.   mAbs

mCSM-AB: a web server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

Novel human IgG1 and IgG4 Fc-engineered antibodies with completely abolished immune effector functions

(2016) Tilman Schlothauer et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Solubis: a webserver to reduce protein aggregation through mutation

(2016) Joost Van Durme et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Loss of Response to Anti-TNFs: Definition, Epidemiology and Management

(2016) Giulia Roda et al.   Clinical and Translational Gastroenterology

The ultimate mix and match: making sense of HLA alleles and peptide repertoires

(2015) David K Cole   IMMUNOLOGY AND CELL BIOLOGY

Evaluating the Use of Antibody Variable Region (Fv) Charge as a Risk Assessment Tool for Predicting Typical Cynomolgus Monkey Pharmacokinetics

(2015) Daniela Bumbaca Yadav et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An overview of bioinformatics tools for epitope prediction: Implications on vaccine development

(2015) Ruth E. Soria-Guerra et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Computational tool for the early screening of monoclonal antibodies for their viscosities

(2015) Neeraj J Agrawal et al.   mAbs

High throughput cross-interaction measures for human IgG1 antibodies correlate with clearance rates in mice

(2015) Ryan L Kelly et al.   mAbs

Balancing charge in the complementarity-determining regions of humanized mAbs without affecting pI reduces non-specific binding and improves the pharmacokinetics

(2015) Amita Datta-Mannan et al.   mAbs

Rational design of viscosity reducing mutants of a monoclonal antibody: Hydrophobicversuselectrostatic inter-molecular interactions

(2015) Pilarin Nichols et al.   mAbs

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry

(2015) Etienne Caron et al.   MOLECULAR & CELLULAR PROTEOMICS

Examination of Thermal Unfolding and Aggregation Profiles of a Series of Developable Therapeutic Monoclonal Antibodies

(2015) Mark L. Brader et al.   MOLECULAR PHARMACEUTICS

A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens

(2015) Joshua Tan et al.   NATURE

Inferring processes underlying B-cell repertoire diversity

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

Charge-mediated influence of the antibody variable domain on FcRn-dependent pharmacokinetics

(2015) Angela Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AB-Bind: Antibody binding mutational database for computational affinity predictions

(2015) Sarah Sirin et al.   PROTEIN SCIENCE

Antibody specific epitope prediction—emergence of a new paradigm

(2015) Inbal Sela-Culang et al.   Current Opinion in Virology

Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences

(2015) Jacob D. Galson et al.   EBioMedicine

PEASE: predicting B-cell epitopes utilizing antibody sequence

(2014) I. Sela-Culang et al.   BIOINFORMATICS

Improving B-cell epitope prediction and its application to global antibody-antigen docking

(2014) Konrad Krawczyk et al.   BIOINFORMATICS

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli

(2014) Narjeskhatoon Habibi et al.   BMC BIOINFORMATICS

Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis

(2014) Johannes Trück et al.   JOURNAL OF IMMUNOLOGY

Freezing-Induced Perturbation of Tertiary Structure of a Monoclonal Antibody

(2014) Lu Liu et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

A general approach to antibody thermostabilization

(2014) Audrey D McConnell et al.   mAbs

Concentration Dependent Viscosity of Monoclonal Antibody Solutions: Explaining Experimental Behavior in Terms of Molecular Properties

(2014) Li Li et al.   PHARMACEUTICAL RESEARCH

In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability

(2014) Vikas K. Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using a Combined Computational-Experimental Approach to Predict Antibody-Specific B Cell Epitopes

(2014) Inbal Sela-Culang et al.   STRUCTURE

Studying the antibody repertoire after vaccination: practical applications

(2014) Jacob D. Galson et al.   TRENDS IN IMMUNOLOGY

Molecular Evolution of Broadly Neutralizing Llama Antibodies to the CD4-Binding Site of HIV-1

(2014) Laura E. McCoy et al.   PLoS Pathogens

IgG Subclasses and Allotypes: From Structure to Effector Functions

(2014) Gestur Vidarsson et al.   Frontiers in Immunology

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server

(2013) Pier Paolo Olimpieri et al.   BIOINFORMATICS

Monoclonal antibody humanness score and its applications

(2013) Sean H Gao et al.   BMC BIOTECHNOLOGY

Evolution and Emergence of Therapeutic Monoclonal Antibodies

(2013) Ian N. Foltz et al.   CIRCULATION

Developability studies before initiation of process development

(2013) Xiaoyu Yang et al.   mAbs

Analytical FcRn affinity chromatography for functional characterization of monoclonal antibodies

(2013) Tilman Schlothauer et al.   mAbs

bNAber: database of broadly neutralizing HIV antibodies

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

SAbDab: the structural antibody database

(2013) James Dunbar 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

A minimal model of peptide binding predicts ensemble properties of serum antibodies

(2012) Victor Greiff et al.   BMC GENOMICS

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

BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

(2012) Jianzhao Gao et al.   PLoS One

An integrated approach to extreme thermostabilization and affinity maturation of an antibody

(2012) A. D. McConnell et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Monoclonal Antibodies with Identical Fc Sequences Can Bind to FcRn Differentially with Pharmacokinetic Consequences

(2011) W. Wang et al.   DRUG METABOLISM AND DISPOSITION

Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes

(2011) Jason Greenbaum et al.   IMMUNOGENETICS

Developability Index: A Rapid In Silico Tool for the Screening of Antibody Aggregation Propensity

(2011) Timothy M. Lauer et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Mutational analysis of domain antibodies reveals aggregation hotspots within and near the complementarity determining regions

(2011) Joseph M. Perchiacca et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

(2010) Shide Liang et al.   BMC BIOINFORMATICS

Importance of Neonatal FcR in Regulating the Serum Half-Life of Therapeutic Proteins Containing the Fc Domain of Human IgG1: A Comparative Study of the Affinity of Monoclonal Antibodies and Fc-Fusion Proteins to Human Neonatal FcR

(2010) Takuo Suzuki et al.   JOURNAL OF IMMUNOLOGY

Potential aggregation prone regions in biotherapeutics

(2010) Xiaoling Wang et al.   mAbs

The immunogenicity of humanized and fully human antibodies

(2010) Fiona A. Harding et al.   mAbs

Exploring Antibody Recognition of Sequence Space through Random-Sequence Peptide Microarrays

(2010) Rebecca F. Halperin et al.   MOLECULAR & CELLULAR PROTEOMICS

Potential Aggregation-Prone Regions in Complementarity-Determining Regions of Antibodies and Their Contribution Towards Antigen Recognition: A Computational Analysis

(2010) Xiaoling Wang et al.   PHARMACEUTICAL RESEARCH

Combinatorial libraries against libraries for selecting neoepitope activation-specific antibodies

(2010) X. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reduced elimination of IgG antibodies by engineering the variable region

(2010) T. Igawa et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Anti-p40 Antibodies Ustekinumab and Briakinumab: Blockade of Interleukin-12 and Interleukin-23 in the Treatment of Psoriasis

(2010) Mona Gandhi et al.   SEMINARS IN CUTANEOUS MEDICINE AND SURGERY

Pharmacokinetic, pharmacodynamic and immunogenicity comparability assessment strategies for monoclonal antibodies

(2010) Wendy S. Putnam et al.   TRENDS IN BIOTECHNOLOGY

Mining for the antibody-antigen interacting associations that predict the B cell epitopes

(2010) Liang Zhao et al.   BMC STRUCTURAL BIOLOGY

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

(2010) Aroop Sircar et al.   PLoS Computational Biology

SOLpro: accurate sequence-based prediction of protein solubility

(2009) Christophe N. Magnan et al.   BIOINFORMATICS

Cross-species Binding Analyses of Mouse and Human Neonatal Fc Receptor Show Dramatic Differences in Immunoglobulin G and Albumin Binding

(2009) Jan Terje Andersen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Population-Based Exposure-Efficacy Modeling of Ustekinumab in Patients With Moderate to Severe Plaque Psoriasis

(2009) Honghui Zhou et al.   JOURNAL OF CLINICAL PHARMACOLOGY

SEPPA: a computational server for spatial epitope prediction of protein antigens

(2009) Jing Sun et al.   NUCLEIC ACIDS RESEARCH

Libraries against libraries for combinatorial selection of replicating antigen-antibody pairs

(2009) D. R. Bowley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of therapeutic proteins with enhanced stability

(2009) N. Chennamsetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

(2008) Michael J. Sweredoski et al.   BIOINFORMATICS

ElliPro: a new structure-based tool for the prediction of antibody epitopes

(2008) Julia Ponomarenko et al.   BMC BIOINFORMATICS

Predicting linear B‐cell epitopes using string kernels

(2008) Yasser EL‐Manzalawy et al.   JOURNAL OF MOLECULAR RECOGNITION

Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility

(2008) Mariana Babor et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS