Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework.

Autor: López CA; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States., Zhang X; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Aydin F; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Shrestha R; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Van QN; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Stanley CB; Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States., Carpenter TS; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Nguyen K; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States., Patel LA; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States., Chen; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Burns V; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States., Hengartner NW; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States., Reddy TJE; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States., Bhatia H; Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Di Natale F; Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Tran TH; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Chan AH; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Simanshu DK; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Nissley DV; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Streitz FH; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Stephen AG; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Turbyville TJ; NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States., Lightstone FC; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Gnanakaran S; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States., Ingólfsson HI; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Neale C; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2022 Aug 09; Vol. 18 (8), pp. 5025-5045. Date of Electronic Publication: 2022 Jul 22.

Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data.

Autor: Jaeger-Honz, Sabrina¹ (AUTHOR) sabrina.jaeger@uni-konstanz.de, Klein, Karsten¹ (AUTHOR), Schreiber, Falk^1,2 (AUTHOR)

Publikováno v: Journal of Cheminformatics. 3/12/2024, Vol. 16 Issue 1, p1-15. 15p.

Obscurin Rho GEF domains are phosphorylated by MST-family kinases but do not exhibit nucleotide exchange factor activity towards Rho GTPases in vitro.

Autor: Koch, Daniel¹ (AUTHOR) dkoch.research@protonmail.com, Kho, Ay Lin¹ (AUTHOR), Fukuzawa, Atsushi¹ (AUTHOR), Alexandrovich, Alexander¹ (AUTHOR), Vanaanen, Kutti J.¹ (AUTHOR), Beavil, Andrew¹ (AUTHOR), Pfuhl, Mark¹ (AUTHOR), Rees, Martin¹ (AUTHOR) dkoch.research@protonmail.com, Gautel, Mathias¹ (AUTHOR) dkoch.research@protonmail.com

Publikováno v: PLoS ONE. 4/20/2023, Vol. 17 Issue 4, p1-23. 23p.

SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction.

Autor: Grosjean, Harold^1,2 (AUTHOR), Işık, Mehtap³ (AUTHOR), Aimon, Anthony^2,4 (AUTHOR), Mobley, David⁵ (AUTHOR), Chodera, John³ (AUTHOR), von Delft, Frank^2,4,6,7 (AUTHOR), Biggin, Philip C¹ (AUTHOR) Philip.biggin@bioch.ox.ac.uk

Publikováno v: Journal of Computer-Aided Molecular Design. Apr2022, Vol. 36 Issue 4, p291-311. 21p.

Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM.

Autor: Bergh, Cathrine, Rovšnik, Urška, Howard, Rebecca, Lindahl, Erik

Publikováno v: eLife; 1/30/2024, p1-18, 18p