Understanding the molecular mechanism of the broad and potent neutralization of HIV-1 by antibody VRC01 from the perspective of molecular dynamics simulation and binding free energy calculations

Electrostatics in proteins and protein–ligand complexes

(2010) Predrag Kukić et al.   Future Medicinal Chemistry

Induction of Immunity to Human Immunodeficiency Virus Type-1 by Vaccination

(2010) M. Juliana McElrath et al.   IMMUNITY

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

Modelling the binding of HIV-reverse transcriptase and nevirapine: an assessment of quantum mechanical and force field approaches and predictions of the effect of mutations on binding

(2010) Rajesh K. Raju et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120

(2010) Ali Emileh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Boost for HIV Vaccine Design

(2010) D. R. Burton et al.   SCIENCE

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

(2010) T. Zhou et al.   SCIENCE

Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1

(2010) X. Wu et al.   SCIENCE

Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity

(2009) Payel Das et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine, and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective

(2009) E. Irene Newhouse et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

(2009) Huanxiang Liu et al.   MOLECULAR PHARMACEUTICS

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

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

Molecular architecture of native HIV-1 gp120 trimers

(2008) Jun Liu et al.   NATURE