Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery

Human Antibodies for Viral Infections

(2022) James E. Crowe   Annual Review of Immunology

Current structure predictors are not learning the physics of protein folding

(2022) Carlos Outeiral et al.   BIOINFORMATICS

ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation

(2022) Brennan Abanades et al.   BIOINFORMATICS

Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics

(2022) Rahul Khetan et al.   mAbs

BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning

(2022) David Prihoda et al.   mAbs

Antibodies to watch in 2022

(2022) Hélène Kaplon et al.   mAbs

A pandemic-enabled comparison of discovery platforms demonstrates a naïve antibody library can match the best immune-sourced antibodies

(2022) Fortunato Ferrara et al.   Nature Communications

Advances in computational structure-based antibody design

(2022) Alissa M. Hummer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2022) Rahmad Akbar et al.   mAbs

In silico proof of principle of machine learning-based antibody design at unconstrained scale

(2022) Rahmad Akbar et al.   mAbs

Antibody-Mediated Drug Delivery

(2021) Fatma Betul Arslan et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

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

Antibodies to watch in 2021

(2021) Hélène Kaplon et al.   mAbs

Deep Sequencing of B Cell Receptor Repertoires From COVID-19 Patients Reveals Strong Convergent Immune Signatures

(2021) Jacob D. Galson et al.   Frontiers in Immunology

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

(2021) Koichiro Saka et al.   Scientific Reports

Public Baseline and shared response structures support the theory of antibody repertoire functional commonality

(2021) Matthew I. J. Raybould et al.   PLoS Computational Biology

Robustification of RosettaAntibody and Rosetta SnugDock

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

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

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

Applications of Machine and Deep Learning in Adaptive Immunity

(2021) Margarita Pertseva et al.   Annual Review of Chemical and Biomolecular Engineering

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

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

(2021) Derek M. Mason et al.   Nature Biomedical Engineering

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

(2021) Claire Marks et al.   BIOINFORMATICS

DLAB—Deep learning methods for structure-based virtual screening of antibodies

(2021) Constantin Schneider et al.   BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Critical Assessment of Methods of Protein Structure Prediction ( CASP ) – Round XIV

(2021) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

epitope3D: a machine learning method for conformational B-cell epitope prediction

(2021) Bruna Moreira da Silva et al.   BRIEFINGS IN BIOINFORMATICS

The trRosetta server for fast and accurate protein structure prediction

(2021) Zongyang Du et al.   Nature Protocols

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

INDI—integrated nanobody database for immunoinformatics

(2021) Piotr Deszyński et al.   NUCLEIC ACIDS RESEARCH

Llamanade: An open-source computational pipeline for robust nanobody humanization

(2021) Zhe Sang et al.   STRUCTURE

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

(2021) Nicolas Renaud et al.   Nature Communications

Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies

(2021) Sarah A. Robinson et al.   PLoS Computational Biology

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

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

(2020) Srivamshi Pittala et al.   BIOINFORMATICS

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

(2020) Yoochan Myung et al.   NUCLEIC ACIDS RESEARCH

Structure-Based Virtual Screening: From Classical to Artificial Intelligence

(2020) Eduardo Habib Bechelane Maia et al.   Frontiers in Chemistry

Phage Display Derived Monoclonal Antibodies: From Bench to Bedside

(2020) Mohamed A. Alfaleh et al.   Frontiers in Immunology

ClonoMatch: a tool for identifying homologous immunoglobulin and T cell receptor sequences in large databases

(2020) Taylor Jones et al.   BIOINFORMATICS

Commonality despite exceptional diversity in the baseline human antibody repertoire

(2019) Bryan Briney et al.   NATURE

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

High frequency of shared clonotypes in human B cell receptor repertoires

(2019) Cinque Soto et al.   NATURE

iScore: A novel graph kernel-based function for scoring protein-protein docking models

(2019) Cunliang Geng et al.   BIOINFORMATICS

Looking for therapeutic antibodies in next-generation sequencing repositories

(2019) Konrad Krawczyk et al.   mAbs

The ABCD database: a repository for chemically defined antibodies

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

Quantifying the nativeness of antibody sequences using long short-term memory networks

(2019) Andrew M Wollacott et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Antibody Complementarity Determining Region Design Using High-Capacity Machine Learning

(2019) Ge Liu et al.   BIOINFORMATICS

Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks

(2019) Xiao Wang et al.   BIOINFORMATICS

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

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

Modeling Antibody-Antigen Complexes by Information-Driven Docking

(2019) Francesco Ambrosetti et al.   STRUCTURE

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

(2018) Edgar Liberis et al.   BIOINFORMATICS

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

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

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

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

(2018) Jared Adolf-Bryfogle et al.   PLoS Computational Biology

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

Structurally Mapping Antibody Repertoires

(2018) Konrad Krawczyk et al.   Frontiers in Immunology

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Biopharmaceutical Informatics: supporting biologic drug development via molecular modelling and informatics

(2017) Sandeep Kumar et al.   JOURNAL OF PHARMACY AND PHARMACOLOGY

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

(2017) Martin Closter Jespersen 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

The H3 loop of antibodies shows unique structural characteristics

(2017) Cristian Regep et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data

(2017) Aleksandr Kovaltsuk et al.   Frontiers in Immunology

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

(2017) Zizhang Sheng et al.   Frontiers in Immunology

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

(2017) Krishna Praneeth Kilambi et al.   Scientific Reports

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

(2016) Jinwoo Leem et al.   mAbs

NAPS: Network Analysis of Protein Structures

(2016) Broto Chakrabarty et al.   NUCLEIC ACIDS RESEARCH

The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility

(2015) Pietro Sormanni et al.   JOURNAL OF MOLECULAR BIOLOGY

The Effect of Small Oligomeric Protein Aggregates on the Immunogenicity of Intravenous and Subcutaneous Administered Antibodies

(2015) Anas M. Fathallah et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Aggregation risk prediction for antibodies and its application to biotherapeutic development

(2015) Olga Obrezanova et al.   mAbs

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

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

(2014) Konrad Krawczyk et al.   BIOINFORMATICS

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies

(2014) K. Yamashita et al.   BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

PyIgClassify: a database of antibody CDR structural classifications

(2014) Jared Adolf-Bryfogle et al.   NUCLEIC ACIDS RESEARCH

OptMAVEn – A New Framework for the de novo Design of Antibody Variable Region Models Targeting Specific Antigen Epitopes

(2014) Tong Li et al.   PLoS One

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

Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization

(2014) Brian D. Weitzner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Second antibody modeling assessment (AMA-II)

(2014) Juan C. Almagro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

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

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

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

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

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

Coupling of Aggregation and Immunogenicity in Biotherapeutics: T- and B-Cell Immune Epitopes May Contain Aggregation-Prone Regions

(2011) Sandeep Kumar et al.   PHARMACEUTICAL RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Impact of Product-Related Factors on Immunogenicity of Biotherapeutics

(2010) Satish Kumar Singh   JOURNAL OF PHARMACEUTICAL SCIENCES

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

(2010) Aroop Sircar et al.   PLoS Computational Biology

RosettaAntibody: antibody variable region homology modeling server

(2009) A. Sircar et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Michael J. Sweredoski et al.   BIOINFORMATICS

PIGS: automatic prediction of antibody structures

(2008) P. Marcatili et al.   BIOINFORMATICS

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

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