Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

Cryo-Electron Microscopy and the Amazing Race to Atomic Resolution

(2015) Elad Binshtein et al.   BIOCHEMISTRY

Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules

(2015) Matteo Levantino et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Distributions of experimental protein structures on coarse-grained free energy landscapes

(2015) Kannan Sankar et al.   JOURNAL OF CHEMICAL PHYSICS

A Structural Mechanism for Calcium Transporter Headpiece Closure

(2015) Nikolai Smolin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

(2015) Sean L. Seyler et al.   PLoS Computational Biology

Accelerated weight histogram method for exploring free energy landscapes

(2014) V. Lindahl et al.   JOURNAL OF CHEMICAL PHYSICS

Sampling large conformational transitions: adenylate kinase as a testing ground

(2014) Sean L. Seyler et al.   MOLECULAR SIMULATION

iMODS: internal coordinates normal mode analysis server

(2014) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

Computing protein dynamics from protein structure with elastic network models

(2014) Ugo Bastolla   Wiley Interdisciplinary Reviews-Computational Molecular Science

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

(2014) Avisek Das et al.   PLoS Computational Biology

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

Exploration of conformational transition pathways from coarse-grained simulations

(2013) Pedro Sfriso et al.   BIOINFORMATICS

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels

(2013) Ludovic Sauguet et al.   EMBO JOURNAL

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

(2013) M. Gur et al.   JOURNAL OF CHEMICAL PHYSICS

Crystal structures of the calcium pump and sarcolipin in the Mg2+-bound E1 state

(2013) Chikashi Toyoshima et al.   NATURE

The sarcolipin-bound calcium pump stabilizes calcium sites exposed to the cytoplasm

(2013) Anne-Marie L. Winther et al.   NATURE

Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography

(2013) G. Gonzalez-Gutierrez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation

(2013) L. Sauguet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PNAS Plus: From the Cover: A gating mechanism of pentameric ligand-gated ion channels

(2013) N. Calimet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings

(2012) Oliver Carrillo et al.   Journal of Chemical Theory and Computation

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

(2012) Pedro Sfriso et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

A locally closed conformation of a bacterial pentameric proton-gated ion channel

(2012) Marie S Prevost et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

(2012) D. M. Kruger et al.   NUCLEIC ACIDS RESEARCH

Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca2+ATPase

(2012) Peter M. Kekenes-Huskey et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Activation Mechanism of SERCA by Calcium

(2011) L. Michel Espinoza-Fonseca et al.   PLoS One

A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks

(2011) Amelie Stein et al.   STRUCTURE

Global Dynamics of Proteins: Bridging Between Structure and Function

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

Approaching Elastic Network Models to Molecular Dynamics Flexibility

(2010) Laura Orellana et al.   Journal of Chemical Theory and Computation

Computing ensembles of transitions from stable states: Dynamic importance sampling

(2010) Juan R. Perilla et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural basis of open channel block in a prokaryotic pentameric ligand-gated ion channel

(2010) Ricarda J C Hilf et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

(2010) H. Nury et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generating stereochemically acceptable protein pathways

(2010) Daniel W. Farrell et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FlexServ: an integrated tool for the analysis of protein flexibility

(2009) J. Camps et al.   BIOINFORMATICS

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

(2009) Lee-Wei Yang et al.   BIOINFORMATICS

A prokaryotic perspective on pentameric ligand-gated ion channel structure

(2009) Ricarda JC Hilf et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

(2009) Barry J. Grant et al.   PLoS Computational Biology

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

(2009) Zheng Yang et al.   PLoS Computational Biology

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics

(2008) Agustí Emperador et al.   BIOPHYSICAL JOURNAL

Can Morphing Methods Predict Intermediate Structures?

(2008) Dahlia R. Weiss et al.   JOURNAL OF MOLECULAR BIOLOGY

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

(2008) S. E. Dobbins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes

(2008) Lei Yang et al.   STRUCTURE