A Multi-Scale–Multi-Stable Model for the Rhodopsin Photocycle

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

(2013) Omar Valsson et al.   Journal of Chemical Theory and Computation

A Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm

(2013) Fabio Trovato et al.   MACROMOLECULES

Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin

(2013) Jin Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Hybrid Molecular Mechanics/Coarse-Grained Calculations Applied to GPCR Receptors

(2012) Capece Luciana et al.   BIOPHYSICAL JOURNAL

Systematic Validation of Protein Force Fields against Experimental Data

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

Effect of channel mutations on the uptake and release of the retinal ligand in opsin

(2012) R. Piechnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

Structural Changes in the N and N′ States of the Bacteriorhodopsin Photocycle

(2009) Deliang Chen et al.   BIOPHYSICAL JOURNAL

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

(2009) Elena Papaleo et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition

(2009) Armida Di Fenza et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The energetics of the primary proton transfer in bacteriorhodopsin revisited: It is a sequential light-induced charge separation after all

(2008) Sonja Braun-Sand et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Coarse-grained force field for the nucleosome from self-consistent multiscaling

(2008) Karine Voltz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY