Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

por Roe, Daniel R., Bergonzo, Christina, Cheatham, Thomas E.
Publicado 2014

On the absence of intra-helical DNA dynamics on the µs to ms timescale

por Galindo-Murillo, Rodrigo, Roe, Daniel R., Cheatham, Thomas E.
Publicado 2014

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

por Bergonzo, Christina, Henriksen, Niel M., Roe, Daniel R., Cheatham, Thomas E.
Publicado 2015

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing

por Thibault, Julien C, Roe, Daniel R, Facelli, Julio C, Cheatham, Thomas E
Publicado 2014

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

por Hayatshahi, Hamed S., Roe, Daniel R., Galindo-Murillo, Rodrigo, Hall, Kathleen B., Cheatham, Thomas E.
Publicado 2016

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

por Bergonzo, Christina, Henriksen, Niel M., Roe, Daniel R., Swails, Jason M., Roitberg, Adrian E., Cheatham, Thomas E.
Publicado 2013

AmberTools

por Case, David A., Aktulga, Hasan Metin, Belfon, Kellon, Cerutti, David S., Cisneros, G. Andrés, Cruzeiro, Vinícius Wilian D., Forouzesh, Negin, Giese, Timothy J., Götz, Andreas W., Gohlke, Holger, Izadi, Saeed, Kasavajhala, Koushik, Kaymak, Mehmet C., King, Edward, Kurtzman, Tom, Lee, Tai-Sung, Li, Pengfei, Liu, Jian, Luchko, Tyler, Luo, Ray, Manathunga, Madushanka, Machado, Matias R., Nguyen, Hai Minh, O’Hearn, Kurt A., Onufriev, Alexey V., Pan, Feng, Pantano, Sergio, Qi, Ruxi, Rahnamoun, Ali, Risheh, Ali, Schott-Verdugo, Stephan, Shajan, Akhil, Swails, Jason, Wang, Junmei, Wei, Haixin, Wu, Xiongwu, Wu, Yongxian, Zhang, Shi, Zhao, Shiji, Zhu, Qiang, Cheatham, Thomas E., Roe, Daniel R., Roitberg, Adrian, Simmerling, Carlos, York, Darrin M., Nagan, Maria C., Merz, Kenneth M.
Publicado 2023