Carlos Simmerling

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 7

Top Topics

Grand Challenge

Multiscale Representation

Experimentally Determined

Top Venues

J. Chem. Inf. Model.

Int. J. Comput. Geom. Appl.

J. Comput. Aided Mol. Des.

Publications

David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
AmberTools. J. Chem. Inf. Model. 63 (20) (2023)
Darya Stepanenko, Stephanie Budhan, Carlos Simmerling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. J. Chem. Inf. Model. 63 (4) (2023)
Lorenzo Casalino, Abigail C. Dommer, Zied Gaieb, Emília P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony T. Bogetti, Austin Clyde, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian T. Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham C. Stern, Lei Huang, John D. McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 35 (5) (2021)
Junjie Zou, Chuan Tian, Carlos Simmerling
Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. J. Comput. Aided Mol. Des. 33 (12) (2019)
Michelle Hatch Hummel, Bihua Yu, Carlos Simmerling, Evangelos A. Coutsias
Laguerre-Intersection Method for Implicit Solvation. Int. J. Comput. Geom. Appl. 28 (1) (2018)
Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos Simmerling, Evangelos A. Coutsias
Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. J. Chem. Inf. Model. 57 (4) (2017)
Michelle Hatch Hummel, Bihua Yu, Carlos Simmerling, Evangelos A. Coutsias
Laguerre-Intersection Method for Implicit Solvation. CoRR (2017)
Kun Song, Viktor Hornak, Carlos De Los Santos, Arthur P. Grollman, Carlos Simmerling
Molecular mechanics parameters for the FapydG DNA lesion. J. Comput. Chem. 29 (1) (2008)
David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods
The Amber biomolecular simulation programs. J. Comput. Chem. 26 (16) (2005)
Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. J. Comput. Chem. 24 (1) (2003)