Thermodynamics and kinetics of large-time-step molecular dynamics

Structure and function of an irreversible agonist-β2 adrenoceptor complex

(2011) Daniel M. Rosenbaum et al.   NATURE

Protein inherent structures by different minimization strategies

(2010) Francesco Rao   JOURNAL OF COMPUTATIONAL CHEMISTRY

Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

(2010) Michele Seeber et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Local Transition Gradients Indicating the Global Attributes of Protein Energy Landscapes

(2010) Francesco Rao   Journal of Physical Chemistry Letters

Conformational Free-Energy Difference of a Miniprotein from Nonequilibrium Simulations

(2010) Martin Spichty et al.   Journal of Physical Chemistry Letters

Protein dynamics investigated by inherent structure analysis

(2010) F. Rao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Force Field Bias in Protein Folding Simulations

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

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

CHARMM: The biomolecular simulation program

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

Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers

(2009) M. Cecchini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Identification of two distinct inactive conformations of the  2-adrenergic receptor reconciles structural and biochemical observations

(2009) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

(2008) Peter L. Freddolino 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

Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations

(2008) Lennart Nilsson   JOURNAL OF COMPUTATIONAL CHEMISTRY

An experimental survey of the transition between two-state and downhill protein folding scenarios

(2008) F. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

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

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY

FACTS: Fast analytical continuum treatment of solvation

(2007) Urs Haberthür et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY