Investigating Substitutions in Antibody–Antigen Complexes Using Molecular Dynamics: A Case Study with Broad-spectrum, Influenza A Antibodies

Novel universal influenza virus vaccine approaches

(2016) Florian Krammer   Current Opinion in Virology

Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin

(2015) Pek Ieong et al.   BIOPHYSICAL JOURNAL

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Advances in the development of influenza virus vaccines

(2015) Florian Krammer et al.   NATURE REVIEWS DRUG DISCOVERY

Broadly Neutralizing Influenza Hemagglutinin Stem-Specific Antibody CR8020 Targets Residues that Are Prone to Escape due to Host Selection Pressure

(2014) Kannan Tharakaraman et al.   Cell Host & Microbe

Rapid development of broadly influenza neutralizing antibodies through redundant mutations

(2014) Leontios Pappas et al.   NATURE

A multiscale approach to predicting affinity changes in protein-protein interfaces

(2014) Daniel F. A. R. Dourado et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular Signatures of Hemagglutinin Stem-Directed Heterosubtypic Human Neutralizing Antibodies against Influenza A Viruses

(2014) Yuval Avnir et al.   PLoS Pathogens

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

(2013) John D. Chodera et al.   Annual Review of Biophysics

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Evolution in the influenza A H3 stalk - a challenge for broad-spectrum vaccines?

(2013) W. D. Lees et al.   JOURNAL OF GENERAL VIROLOGY

Free-Energy Simulations Reveal that Both Hydrophobic and Polar Interactions Are Important for Influenza Hemagglutinin Antibody Binding

(2012) Zhen Xia et al.   BIOPHYSICAL JOURNAL

Multiscale modeling of macromolecular biosystems

(2012) S. C. Flores et al.   BRIEFINGS IN BIOINFORMATICS

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

(2012) R. Burke Squires et al.   Influenza and Other Respiratory Viruses

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Highly Conserved Protective Epitopes on Influenza B Viruses

(2012) C. Dreyfus et al.   SCIENCE

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

A Highly Conserved Neutralizing Epitope on Group 2 Influenza A Viruses

(2011) D. C. Ekiert et al.   SCIENCE

Thermodynamics of Ligand Binding and Efficiency

(2011) Charles H. Reynolds et al.   ACS Medicinal Chemistry Letters

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Structure-Activity Relationships in Peptide-Antibody Complexes: Implications for Epitope Prediction and Development of Synthetic Peptide Vaccines

(2009) Shu-wen Chen et al.   CURRENT MEDICINAL CHEMISTRY

How to obtain statistically converged MM/GBSA results

(2009) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals

(2009) Johannes F. Scheid et al.   NATURE

Antibody Recognition of a Highly Conserved Influenza Virus Epitope

(2009) D. C. Ekiert et al.   SCIENCE

Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet

(2008) Yasmina Abdiche et al.   ANALYTICAL BIOCHEMISTRY

Single Mutation Induced H3N2 Hemagglutinin Antibody Neutralization: A Free Energy Perturbation Study

(2008) Ruhong Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Heterosubtypic Neutralizing Monoclonal Antibodies Cross-Protective against H5N1 and H1N1 Recovered from Human IgM+ Memory B Cells

(2008) Mark Throsby et al.   PLoS One

Computational characterization of B-cell epitopes

(2007) Nimrod D. Rubinstein et al.   MOLECULAR IMMUNOLOGY