QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts von Ribeiro, João V., Bernardi, Rafael C., Rudack, Till, Stone, John E., Phillips, James C., Freddolino, Peter L., Schulten, Klaus

Volltext

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD von Jiang, Wei, Hardy, David J, Phillips, James C, MacKerell, Alexander D, Schulten, Klaus, Roux, Benoît

Volltext

Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome von Zeng, Fuxing, Chen, Yanbo, Remis, Jonathan, Shekhar, Mrinal, Phillips, James C., Tajkhorshid, Emad, Jin, Hong

Volltext

DATA-DRIVEN ORIGINALISM von Lee, Thomas R., Phillips, James C.

Volltext

GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations von Tanner, David E, Phillips, James C, Schulten, Klaus

Volltext

Scalable molecular dynamics on CPU and GPU architectures with NAMD von 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

Volltext

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems von Radak, Brian K, Chipot, Christophe, Suh, Donghyuk, Jo, Sunhwan, Jiang, Wei, Phillips, James C, Schulten, Klaus, Roux, Benoît

Volltext

Why and how did the COVID pandemic end abruptly? von Moret, Marcelo A., Phillips, James C.

Volltext

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism von Singharoy, Abhishek, Maffeo, Christopher, Delgado-Magnero, Karelia H., Swainsbury, David J.K., Sener, Melih, Kleinekathöfer, Ulrich, Vant, John W., Nguyen, Jonathan, Hitchcock, Andrew, Isralewitz, Barry, Teo, Ivan, Chandler, Danielle E., Stone, John E., Phillips, James C., Pogorelov, Taras V., Mallus, M. Ilaria, Chipot, Christophe, Luthey-Schulten, Zaida, Tieleman, D. Peter, Hunter, C. Neil, Tajkhorshid, Emad, Aksimentiev, Aleksei, Schulten, Klaus

Volltext

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD von Jiang, Wei, Phillips, James C., Huang, Lei, Fajer, Mikolai, Meng, Yilin, Gumbart, James C., Luo, Yun, Schulten, Klaus, Roux, Benoît

Volltext

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules von Comer, Jeffrey, Phillips, James C, Schulten, Klaus, Chipot, Christophe

Volltext

The challenges of theory-software translation [version 1; peer review: 2 approved, 1 approved with reservations] von Jay, Caroline, Haines, Robert, Katz, Daniel S, Carver, Jeffrey C, Gesing, Sandra, Brandt, Steven R, Howison, James, Dubey, Anshu, Phillips, James C, Wan, Hui, Turk, Matthew J

Volltext

Molecular Dynamics Simulations of Discoidal Bilayers Assembled from Truncated Human Lipoproteins von Shih, Amy Y., Denisov, Ilia G., Phillips, James C., Sligar, Stephen G., Schulten, Klaus

Volltext

AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD von Antolínez, Santiago, Jones, Peter Eugene, Phillips, James C., Hadden-Perilla, Jodi A.

Volltext

Scalable molecular dynamics with NAMD von Phillips, James C., Braun, Rosemary, Wang, Wei, Gumbart, James, Tajkhorshid, Emad, Villa, Elizabeth, Chipot, Christophe, Skeel, Robert D., Kalé, Laxmikant, Schulten, Klaus

Volltext

Parallel Generalized Born Implicit Solvent Calculations with NAMD von Tanner, David E, Chan, Kwok-Yan, Phillips, James C, Schulten, Klaus

Volltext

Why Aβ42 Is Much More Toxic than Aβ40 von Phillips, James C

Volltext

Accelerating molecular modeling applications with graphics processors von Stone, John E, Phillips, James C, Freddolino, Peter L, Hardy, David J, Trabuco, Leonardo G, Schulten, Klaus

Volltext

Revealing the Effect of Irradiation on Cement Hydrates: Evidence of a Topological Self-Organization von Krishnan, N. M. Anoop, Wang, Bu, Sant, Gaurav, Phillips, James C, Bauchy, Mathieu

Volltext

stringent test for hydrophobicity scales: Two proteins with 88% sequence identity but different structure and function von Kister, Alexander E, Phillips, James C

Volltext