Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

The Dynamic Process of β2-Adrenergic Receptor Activation

(2013) Rie Nygaard et al.   CELL

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Science in the Cloud: Accelerating Discovery in the 21st Century

(2012) Joseph L. Hellerstein et al.   IEEE INTERNET COMPUTING

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

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

Structure-based drug screening for G-protein-coupled receptors

(2012) Brian K. Shoichet et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Efficacy of the β2-adrenergic receptor is determined by conformational equilibrium in the transmembrane region

(2012) Yutaka Kofuku et al.   Nature Communications

Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors

(2011) Edgar A. Gatica et al.   Journal of Chemical Information and Modeling

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Structure of a nanobody-stabilized active state of the β2 adrenoceptor

(2011) Søren G. F. Rasmussen et al.   NATURE

Structure and function of an irreversible agonist-β2 adrenoceptor complex

(2011) Daniel M. Rosenbaum et al.   NATURE

Crystal structure of the β2 adrenergic receptor–Gs protein complex

(2011) Søren G. F. Rasmussen et al.   NATURE

Activation mechanism of the  2-adrenergic receptor

(2011) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

(2011) Stefano Vanni et al.   PLoS Computational Biology

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

(2009) Alexander Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

(2009) P. W. Hildebrand et al.   NUCLEIC ACIDS RESEARCH

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Bigtable

(2008) Fay Chang et al.   ACM TRANSACTIONS ON COMPUTER SYSTEMS

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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