Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations

(2013) Peichen Pan et al.   ANTIVIRAL RESEARCH

Computational and experimental analysis of drug binding to the Influenza M2 channel

(2013) Raphael Alhadeff et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development

(2013) Chinh TT Su et al.   BMC BIOINFORMATICS

Macromolecular Structure Comparison and Docking: An Algorithmic Review

(2013) Eric Paquet et al.   CURRENT PHARMACEUTICAL DESIGN

Exploring the Proton Conductance and Drug Resistance of BM2 Channel through Molecular Dynamics Simulations and Free Energy Calculations at Different pH Conditions

(2013) Yuxin Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring Histidine Conformations in the M2 Channel Lumen of the Influenza A Virus at Neutral pH via Molecular Simulations

(2013) Hao Dong et al.   Journal of Physical Chemistry Letters

Rational Epitope Design for Protein Targeting

(2012) Claudio Peri et al.   ACS Chemical Biology

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding

(2012) Bogdan Tarus et al.   PLoS One

Influenza virus binds its host cell using multiple dynamic interactions

(2012) C. Sieben et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex

(2012) Cyril F. Reboul et al.   PLoS Computational Biology

Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope

(2011) Ayşegül Özen et al.   JOURNAL OF MOLECULAR BIOLOGY

Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations

(2011) Nan-jie Deng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Dynamics Simulation Directed Rational Design of Inhibitors Targeting Drug-Resistant Mutants of Influenza A Virus M2

(2011) Jun Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High performance screening, structural and molecular dynamics analysis to identify H1 inhibitors from TCM Database@Taiwan

(2011) Su-Sen Chang et al.   Molecular BioSystems

Mechanism of 150-cavity formation in influenza neuraminidase

(2011) Rommie E. Amaro et al.   Nature Communications

Top Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach

(2010) Binh Khanh Mai et al.   Journal of Chemical Information and Modeling

Efficient stochastic thermostatting of path integral molecular dynamics

(2010) Michele Ceriotti et al.   JOURNAL OF CHEMICAL PHYSICS

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

(2010) Ron O. Dror et al.   JOURNAL OF GENERAL PHYSIOLOGY

Prediction of zanamivir efficiency over the possible 2009 Influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations

(2010) Dabo Pan et al.   JOURNAL OF MOLECULAR MODELING

The binding properties of the H5N1 influenza virus neuraminidase as inferred from molecular modeling

(2010) Michal Raab et al.   JOURNAL OF MOLECULAR MODELING

Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus

(2010) Mao Shu et al.   JOURNAL OF MOLECULAR MODELING

Synergistic effects in the designs of neuraminidase ligands: Analysis from docking and molecular dynamics studies

(2010) Zhiwei Yang et al.   JOURNAL OF THEORETICAL BIOLOGY

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy

(2010) Morgan Lawrenz et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases

(2010) Ly Le et al.   PLoS Computational Biology

Molecular prediction of oseltamivir efficiency against probable influenza A (H1N1-2009) mutants: molecular modeling approach

(2009) Thanyada Rungrotmongkol et al.   AMINO ACIDS

Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A(H1N1) influenza neuraminidase

(2009) Yeng-Tseng Wang et al.   BIOPHYSICAL CHEMISTRY

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Distinct Glycan Topology for Avian and Human Sialopentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective

(2009) Dong Xu et al.   JOURNAL OF MOLECULAR BIOLOGY

Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations

(2009) Martin Klvana et al.   JOURNAL OF MOLECULAR BIOLOGY

Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations

(2009) Rommie E. Amaro 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

Molecular simulations of protein dynamics: new windows on mechanisms in biology

(2008) Guy G Dodson et al.   EMBO REPORTS

Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins

(2008) Giulia Morra et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Dynamical Spatial Warping: A Novel Method for the Conformational Sampling of Biophysical Structure

(2008) Peter Minary et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING