A generalized linear response framework for expanded ensemble and replica exchange simulations
Radak, Brian K, Suh, Donghyuk, Roux, Benoît
Published in The Journal of chemical physics (21.08.2018)
Published in The Journal of chemical physics (21.08.2018)
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Journal Article
Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation
Gu, Hong, Zhang, Shuming, Wong, Kin-Yiu, Radak, Brian K., Dissanayake, Thakshila, Kellerman, Daniel L., Dai, Qing, Miyagi, Masaru, Anderson, Vernon E., York, Darrin M., Piccirilli, Joseph A., Harris, Michael E.
Published in Proceedings of the National Academy of Sciences - PNAS (06.08.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (06.08.2013)
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A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields
Giese, Timothy J, Chen, Haoyuan, Dissanayake, Thakshila, Giambaşu, George M, Heldenbrand, Hugh, Huang, Ming, Kuechler, Erich R, Lee, Tai-Sung, Panteva, Maria T, Radak, Brian K, York, Darrin M
Published in Journal of chemical theory and computation (12.03.2013)
Published in Journal of chemical theory and computation (12.03.2013)
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Journal Article
Rigorous Free Energy Simulations in Virtual Screening
Cournia, Zoe, Allen, Bryce K, Beuming, Thijs, Pearlman, David A, Radak, Brian K, Sherman, Woody
Published in Journal of chemical information and modeling (28.09.2020)
Published in Journal of chemical information and modeling (28.09.2020)
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Journal Article
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery
Lee, Tai-Sung, Allen, Bryce K, Giese, Timothy J, Guo, Zhenyu, Li, Pengfei, Lin, Charles, McGee, T. Dwight, Pearlman, David A, Radak, Brian K, Tao, Yujun, Tsai, Hsu-Chun, Xu, Huafeng, Sherman, Woody, York, Darrin M
Published in Journal of chemical information and modeling (23.11.2020)
Published in Journal of chemical information and modeling (23.11.2020)
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Journal Article
Scalable molecular dynamics on CPU and GPU architectures with NAMD
Phillips, James C, Hardy, David J, Maia, Julio D C, Stone, John E, Ribeiro, João V, Bernardi, Rafael C, Buch, Ronak, Fiorin, Giacomo, Hénin, Jérôme, Jiang, Wei, McGreevy, Ryan, Melo, Marcelo C R, Radak, Brian K, Skeel, Robert D, Singharoy, Abhishek, Wang, Yi, Roux, Benoît, Aksimentiev, Aleksei, Luthey-Schulten, Zaida, Kalé, Laxmikant V, Schulten, Klaus, Chipot, Christophe, Tajkhorshid, Emad
Published in The Journal of chemical physics (28.07.2020)
Published in The Journal of chemical physics (28.07.2020)
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Accounting for the Central Role of Interfacial Water in Protein–Ligand Binding Free Energy Calculations
Ben-Shalom, Ido Y, Lin, Zhixiong, Radak, Brian K, Lin, Charles, Sherman, Woody, Gilson, Michael K
Published in Journal of chemical theory and computation (08.12.2020)
Published in Journal of chemical theory and computation (08.12.2020)
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Journal Article
Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials
Lee, Tai-Sung, Lin, Zhixiong, Allen, Bryce K, Lin, Charles, Radak, Brian K, Tao, Yujun, Tsai, Hsu-Chun, Sherman, Woody, York, Darrin M
Published in Journal of chemical theory and computation (08.09.2020)
Published in Journal of chemical theory and computation (08.09.2020)
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Journal Article
Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units
Ben-Shalom, Ido Y, Lin, Charles, Radak, Brian K, Sherman, Woody, Gilson, Michael K
Published in Journal of chemical theory and computation (14.12.2021)
Published in Journal of chemical theory and computation (14.12.2021)
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Journal Article
Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences
Li, Pengfei, Li, Zhijie, Wang, Yu, Dou, Huaixia, Radak, Brian K, Allen, Bryce K, Sherman, Woody, Xu, Huafeng
Published in Journal of chemical theory and computation (08.02.2022)
Published in Journal of chemical theory and computation (08.02.2022)
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Journal Article
A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation
Lee, Tai-Sung, Radak, Brian K, Harris, Michael E, York, Darrin M
Published in ACS catalysis (04.03.2016)
Published in ACS catalysis (04.03.2016)
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Journal Article
Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
Radak, Brian K, Chipot, Christophe, Suh, Donghyuk, Jo, Sunhwan, Jiang, Wei, Phillips, James C, Schulten, Klaus, Roux, Benoît
Published in Journal of chemical theory and computation (11.12.2018)
Published in Journal of chemical theory and computation (11.12.2018)
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