Molecular insight on the binding of NNRTI to K103N mutated HIV-1 RT: molecular dynamics simulations and dynamic pharmacophore analysis

QSAR models and scaffold-based analysis of non-nucleoside HIV RT inhibitors

(2015) Bilal Nizami et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Structural Characteristics of the Allosteric Binding Site Represent a Key to Subtype Selective Modulators of Muscarinic Acetylcholine Receptors

(2015) Marcel Bermudez et al.   Molecular Informatics

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase

(2013) Daniel G. Kuroda et al.   Nature Chemistry

High-Levels of Acquired Drug Resistance in Adult Patients Failing First-Line Antiretroviral Therapy in a Rural HIV Treatment Programme in KwaZulu-Natal, South Africa

(2013) Justen Manasa et al.   PLoS One

Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and resistance by connection mutations

(2013) R. S. K. Vijayan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Increases in Adult Life Expectancy in Rural South Africa: Valuing the Scale-Up of HIV Treatment

(2013) J. Bor et al.   SCIENCE

Ion condensation behavior and dynamics of water molecules surrounding the sodium poly(methacrylic acid) chain in water: A molecular dynamics study

(2012) Yung-Ting Chung et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase

(2012) David W. Wright et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

(2011) Peter Schmidtke et al.   BIOINFORMATICS

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Crystal Structures of HIV-1 Reverse Transcriptase with Etravirine (TMC125) and Rilpivirine (TMC278): Implications for Drug Design

(2010) Eric B. Lansdon et al.   JOURNAL OF MEDICINAL CHEMISTRY

Adult mortality and antiretroviral treatment roll-out in rural KwaZulu-Natal, South Africa

(2009) Abraham J Herbst et al.   BULLETIN OF THE WORLD HEALTH ORGANIZATION

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: Strategic flexibility explains potency against resistance mutations

(2008) K. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA