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

Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction

(2020) Maxim Shapovalov et al.   PLoS One

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells

(2020) Yunlong Cao et al.   CELL

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

(2020) Davide F. Robbiani et al.   NATURE

Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

(2020) Alina Baum et al.   SCIENCE

Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model

(2020) Thomas F. Rogers et al.   SCIENCE

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy

(2020) Shuo Du et al.   CELL

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes

(2020) Tal Noy-Porat et al.   Nature Communications

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

(2020) Nicholas C. Wu et al.   PLoS Pathogens

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

(2019) Carlos H M Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design

(2019) Daniel A. Cannon et al.   PLoS Computational Biology

Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces

(2019) Shira Warszawski et al.   PLoS Computational Biology

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

(2019) Richard A Norman et al.   BRIEFINGS IN 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

Fast Calculation of Protein–Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model

(2018) Jagdish Suresh Patel et al.   Journal of Chemical Theory and Computation

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

OSPREY 3.0: Open-source protein redesign for you, with powerful new features

(2018) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

(2018) Cunliang Geng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts

(2017) Peng Xiong et al.   JOURNAL OF MOLECULAR BIOLOGY

SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations

(2016) Marharyta Petukh et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

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

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

(2015) Sarah Sirin et al.   PROTEIN SCIENCE

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

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

Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins

(2014) Joe DeBartolo et al.   PLoS Computational Biology

ECOD: An Evolutionary Classification of Protein Domains

(2014) Hua Cheng et al.   PLoS Computational Biology

Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys

(2013) Dan H. Barouch et al.   NATURE

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

(2012) Iain H. Moal et al.   BIOINFORMATICS

Alternative Protein-Protein Interfaces Are Frequent Exceptions

(2012) Tobias Hamp et al.   PLoS Computational Biology

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Quantitation of protein-protein interactions by thermal stability shift analysis

(2011) Curtis J. Layton et al.   PROTEIN SCIENCE

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Escape from Human Monoclonal Antibody Neutralization Affects In Vitro and In Vivo Fitness of Severe Acute Respiratory Syndrome Coronavirus

(2010) Barry Rockx et al.   JOURNAL OF INFECTIOUS DISEASES

Challenges in the computational design of proteins

(2009) M. Suarez et al.   Journal of the Royal Society Interface

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design

(2008) Elisabeth L. Humphris et al.   STRUCTURE

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE