Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation

Molecular Dynamics Simulation of the Unfolding of Individual Bacteriorhodopsin Helices in Sodium Dodecyl Sulfate Micelles

(2012) Venkatramanan Krishnamani et al.   BIOCHEMISTRY

Secondary and Tertiary Structure of Bacteriorhodopsin in the SDS Denatured State

(2012) Venkatramanan Krishnamani et al.   BIOCHEMISTRY

Computer simulation studies of self-assembling macromolecules

(2012) Wataru Shinoda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

(2012) Mikyung Seo et al.   Journal of Chemical Theory and Computation

Coarse-Grained and Atomistic Simulations of the Salt-Stable Cowpea Chlorotic Mottle Virus (SS-CCMV) Subunit 26–49: β-Barrel Stability of the Hexamer and Pentamer Geometries

(2012) Tristan Bereau et al.   Journal of Chemical Theory and Computation

Line-Tension Controlled Mechanism for Influenza Fusion

(2012) Herre Jelger Risselada et al.   PLoS One

Mechanism of Voltage Gating in Potassium Channels

(2012) M. O. Jensen et al.   SCIENCE

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions

(2011) Jia-Wei Shen et al.   Journal of Chemical Theory and Computation

The future of molecular dynamics simulations in drug discovery

(2011) David W. Borhani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structural modeling and molecular dynamics simulation of the actin filament

(2011) Thomas Splettstoesser et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

(2010) Freddie R Salsbury Jr   CURRENT OPINION IN PHARMACOLOGY

QM/MM Approaches in Medicinal Chemistry Research

(2010) Lochana Menikarachchi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Molecular simulations of ion channels: a quantum chemist’s perspective

(2010) Denis Bucher et al.   JOURNAL OF GENERAL PHYSIOLOGY

Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85

(2010) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1

(2010) T. Shimamura et al.   SCIENCE

Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling

(2009) Alessio Lodola et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Elucidating the Mechanism behind Irreversible Deformation of Viral Capsids

(2009) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study

(2009) Mareike Zink et al.   BIOPHYSICAL JOURNAL

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

(2009) Sason Shaik et al.   CHEMICAL REVIEWS

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex

(2008) Michel A. Cuendet et al.   BIOPHYSICAL JOURNAL

Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

(2008) Edward Lyman et al.   BIOPHYSICAL JOURNAL

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation