Scientific Publications

  1. 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. Kalé, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid. J. Chem. Phys. 153, 044130, 2020
  2. Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons. Yuhang Wang, Mrinal Shekhar, Darren Thifault, Christopher J. Williams, Ryan McGreevy, Jane Richardson, Abhishek Singharoy, Emad Tajkhorshid. Journal of Structural Biology, 204:319-328, 2018.
  3. CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. Yifei Qi, Jumin Lee, Abhishek Singharoy, Ryan McGreevy, Klaus Schulten, and Wonpil Im. The Journal of Physical Chemistry B, 2016.
  4. Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps. Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao and Klaus Schulten. eLife, 2016.
  5. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Boon Chong Goh, Jodi A. Hadden, Rafael C. Bernardi, Abhishek Singharoy, Ryan McGreevy, Till Rudack, C. Keith Cassidy and Klaus Schulten. Annual Review of Biophysics, 45, 2016
  6. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Ryan McGreevy, Ivan Teo, Abhishek Singharoy and Klaus Schulten. Methods, 100:50-60, 2016
  7. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures. Ryan McGreevy,  Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo and Klaus Schulten. Acta Cryst. D, 70:2344-2355, 2014
  8. GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting. John E. Stone, Ryan McGreevy, Barry Isralewitz and Klaus Schulten. Faraday Disc., 169:265-283, 2014 (Chosen for journal cover image)
  9. 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, Benoit Roux, Klaus Schulten, Anthony Kossiakoff and Eduardo Perozo. Nat. Struct. & Mol. Biol., 21:244-252, 2014
  10. Symmetry-restrained flexible fitting for symmetric EM maps. Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell and Klaus Schulten. Structure, 19:1211-1218, 2011.