On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

(2010) Olivier Sperandio et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

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

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

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

(2009) Gary S. Ayton et al.   FARADAY DISCUSSIONS

Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR)

(2009) Nicolas Floquet et al.   JOURNAL OF MOLECULAR BIOLOGY

Transport mechanism of a bacterial homologue of glutamate transporters

(2009) Nicolas Reyes et al.   NATURE

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

(2009) A. Bakan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter

(2009) Yan Gu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inward-facing conformation of glutamate transporters as revealed by their inverted-topology structural repeats

(2009) T. J. Crisman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

(2009) Zheng Yang et al.   PLoS Computational Biology

Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes

(2008) Nigar Kantarci-Carsibasi et al.   BIOPHYSICAL JOURNAL

Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes

(2008) Basak Isin et al.   BIOPHYSICAL JOURNAL

Time-resolved Mechanism of Extracellular Gate Opening and Substrate Binding in a Glutamate Transporter

(2008) Indira H. Shrivastava et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Normal mode partitioning of Langevin dynamics for biomolecules

(2008) Christopher R. Sweet et al.   JOURNAL OF CHEMICAL PHYSICS

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

(2008) Andreas May et al.   JOURNAL OF MEDICINAL CHEMISTRY

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL

(2008) Chakra Chennubhotla et al.   Molecular BioSystems

Crystal structure of the ligand-free G-protein-coupled receptor opsin

(2008) Jung Hee Park et al.   NATURE

Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel

(2008) Ricarda J. C. Hilf et al.   NATURE

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

(2008) Nicolas Bocquet et al.   NATURE

Structural analysis of ion selectivity in the NaK channel

(2008) Amer Alam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Principles of flexible protein-protein docking

(2008) Nelly Andrusier et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE