R
Ryan McGreevy
Researcher at University of Illinois at Urbana–Champaign
Publications - 11
Citations - 1888
Ryan McGreevy is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Visualization & Protein Data Bank. The author has an hindex of 9, co-authored 11 publications receiving 910 citations. Previous affiliations of Ryan McGreevy include University of Illinois at Chicago.
Papers
More filters
Journal ArticleDOI
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C. Phillips,David J. Hardy,Julio D.C. Maia,John E. Stone,João V. Ribeiro,Rafael C. Bernardi,Ronak Buch,Giacomo Fiorin,Jérôme Hénin,Wei Jiang,Ryan McGreevy,Marcelo C. R. Melo,Brian K. Radak,Robert D. Skeel,Abhishek Singharoy,Yi Wang,Benoît Roux,Aleksei Aksimentiev,Zaida Luthey-Schulten,Laxmikant V. Kale,Klaus Schulten,Christophe Chipot,Emad Tajkhorshid +22 more
TL;DR: The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
Journal ArticleDOI
Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain
Qufei Li,Sherry Wanderling,Marcin Paduch,David Medovoy,Abhishek Singharoy,Ryan McGreevy,Carlos A. Villalba-Galea,Raymond E. Hulse,Benoît Roux,Klaus Schulten,Anthony A. Kossiakoff,Eduardo Perozo +11 more
TL;DR: Crystal structures of the Ciona intestinalis VSD (Ci-VSD) are determined in putatively active and resting conformations and provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent enzymes and ion channels.
Journal ArticleDOI
Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
TL;DR: Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures.
Journal ArticleDOI
Advances in the molecular dynamics flexible fitting method for cryo-EM modeling.
TL;DR: The current article serves as an overview of the strategies that have been developed since MDFF's inception to overcome common challenges and successfully perform MDFF simulations.
Journal ArticleDOI
Symmetry-Restrained Flexible Fitting for Symmetric EM Maps
Kwok Yan Chan,James C. Gumbart,Ryan McGreevy,Jean M. Watermeyer,B. Trevor Sewell,Klaus Schulten +5 more
TL;DR: The symmetry-restrained MDFF method is developed, which adds to the cryo-EM map-derived potential further restraints on the allowed conformations of a complex during fitting, thereby improving the quality of the resultant structure.