Carlos Simmerling

According to our database, Carlos Simmerling authored at least 10 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.

Jason T. Linzer, Ethan Aminov, Aalim S. Abdullah, Colleen E. Kirkup, Rebeca I. Diaz Ventura, Vinay R. Bijoor, Jiyun Jung, Sophie Huang, Chi Gee Tse, Emily Álvarez Toucet, Hugo P. Onghai, Arghya P. Ghosh, Alex C. Grodzki, Emilee R. Haines, Aditya S. Iyer, Mark K. Khalil, Alexander P. Leong, Michael A. Neuhaus, Joseph Park, Asir Shahid, Matthew Xie, Jan M. Ziembicki, Carlos Simmerling, Maria C. Nagan

J. Chem. Inf. Model., 2024

2023

AmberTools.

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.

J. Chem. Inf. Model., October, 2023

SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein.

Darya Stepanenko, Stephanie Budhan, Carlos Simmerling

J. Chem. Inf. Model., February, 2023

2021

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.

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

Int. J. High Perform. Comput. Appl., 2021

2019

Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4.

Junjie Zou, Chuan Tian, Carlos Simmerling

J. Comput. Aided Mol. Des., 2019

2018

Laguerre-Intersection Method for Implicit Solvation.

Michelle Hatch Hummel, Bihua Yu, Carlos Simmerling, Evangelos A. Coutsias

Int. J. Comput. Geom. Appl., 2018

2017

Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis.

Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos Simmerling, Evangelos A. Coutsias

J. Chem. Inf. Model., 2017

2008

Molecular mechanics parameters for the FapydG DNA lesion.

Kun Song, Viktor Hornak, Carlos De Los Santos, Arthur P. Grollman, Carlos Simmerling

J. Comput. Chem., 2008

2005

The Amber biomolecular simulation programs.

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

J. Comput. Chem., 2005

2003

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.

Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling

J. Comput. Chem., 2003