GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

(2015) Michael Feig et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations

(2014) Jaewoon Jung et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

(2014) I. Ohmura et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Phase segregation in bio-inspired multi-component vesicles encompassing double tail phospholipid species

(2014) Fikret Aydin et al.   Soft Matter

Coarse-Graining Methods for Computational Biology

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

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems

(2013) Takaharu Mori et al.   Journal of Chemical Theory and Computation

PRIMO: A Transferable Coarse-Grained Force Field for Proteins

(2013) Parimal Kar et al.   Journal of Chemical Theory and Computation

MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms

(2013) Yoshimichi Andoh et al.   Journal of Chemical Theory and Computation

New faster CHARMM molecular dynamics engine

(2013) Antti-Pekka Hynninen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient lookup table using a linear function of inverse distance squared

(2013) Jaewoon Jung et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Reaching new levels of realism in modeling biological macromolecules in cellular environments

(2013) Michael Feig et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Large effect of membrane tension on the fluid-solid phase transitions of two-component phosphatidylcholine vesicles

(2013) D. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Who Will Step Up to Exascale?

(2013) R. F. Service   SCIENCE

The power of coarse graining in biomolecular simulations

(2013) Helgi I. Ingólfsson et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Increasing Membrane Tension Decreases Miscibility Temperatures; an Experimental Demonstration via Micropipette Aspiration

(2012) Thomas Portet et al.   BIOPHYSICAL JOURNAL

Phase Behavior of Lipid Bilayers under Tension

(2012) Mark J. Uline et al.   BIOPHYSICAL JOURNAL

Coarse-grained molecular simulations of large biomolecules

(2012) Shoji Takada   CURRENT OPINION IN STRUCTURAL BIOLOGY

Computational studies of molecular machines: the ribosome

(2012) Karissa Y Sanbonmatsu   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

(2012) Satoru G. Itoh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Transmembrane Helix Assembly by Window Exchange Umbrella Sampling

(2012) Soohyung Park et al.   PHYSICAL REVIEW LETTERS

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

(2011) Hiroo Kenzaki et al.   Journal of Chemical Theory and Computation

Lateral phase separation in tense membranes

(2011) Tsutomu Hamada et al.   Soft Matter

Recent developments and applications of the CHARMM force fields

(2011) Xiao Zhu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation

(2010) Michael Feig et al.   BIOPHYSICAL JOURNAL

Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules

(2010) Satoru G. Itoh et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses

(2010) E. Prabhu Raman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms

(2010) Yoshiharu Mori et al.   JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN

Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble

(2010) Yoshiharu Mori et al.   JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

(2010) T. Ando et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

CHARMM: The biomolecular simulation program

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

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of the Protein-Conducting Channel by a Bound Ribosome

(2009) James Gumbart et al.   STRUCTURE

Computational techniques for efficient conformational sampling of proteins

(2008) Adam Liwo et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2008) Lennart Nilsson   JOURNAL OF COMPUTATIONAL CHEMISTRY

GPU Computing

(2008) J.D. Owens et al.   PROCEEDINGS OF THE IEEE

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Raft Composition at Physiological Temperature and pH in the Absence of Detergents

(2007) Artem G. Ayuyan et al.   BIOPHYSICAL JOURNAL