Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics

(2019) Mangesh Damre et al.   NUCLEIC ACIDS RESEARCH

Integrative modeling of the HIV-1 ribonucleoprotein complex

(2019) David S. Goodsell et al.   PLoS Computational Biology

Minimal coarse-grained models for molecular self-organisation in biology

(2019) Anne E Hafner et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Reproducibility of clinical research in critical care: a scoping review

(2018) Daniel J. Niven et al.   BMC Medicine

Coarse-grained simulation of DNA using LAMMPS

(2018) Oliver Henrich et al.   EUROPEAN PHYSICAL JOURNAL E

Instant Construction and Visualization of Crowded Biological Environments

(2018) Tobias Klein et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Lattice Models of Bacterial Nucleoids

(2018) David S. Goodsell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments

(2018) Harshwardhan H. Katkar et al.   BIOPHYSICAL JOURNAL

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Advances in coarse-grained modeling of macromolecular complexes

(2018) Alexander J Pak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

(2017) James A. Graham et al.   Journal of Chemical Information and Modeling

Modeling chemical reactions in classical molecular dynamics simulations

(2017) Jacob R. Gissinger et al.   POLYMER

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

(2016) Brad A. Krajina et al.   BIOPHYSICAL JOURNAL

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

(2015) Benedict E. K. Snodin et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

(2015) Yifei Qi et al.   Journal of Chemical Theory and Computation

Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation

(2015) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape

(2015) Lam T. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

cellPACK: a virtual mesoscope to model and visualize structural systems biology

(2014) Graham T Johnson et al.   NATURE METHODS

Coarse-Graining Methods for Computational Biology

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

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Organization and segregation of bacterial chromosomes

(2013) Xindan Wang et al.   NATURE REVIEWS GENETICS

Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement

(2013) S.-H. Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The power of coarse graining in biomolecular simulations

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

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

(2011) Alpeshkumar K. Malde et al.   Journal of Chemical Theory and Computation

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Water Modeled As an Intermediate Element between Carbon and Silicon†

(2008) Valeria Molinero et al.   JOURNAL OF PHYSICAL CHEMISTRY B