Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials.

Autor: Sabanés Zariquiey F; Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain.; Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain., Galvelis R; Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain.; Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain., Gallicchio E; Department of Chemistry, Graduate Center, Brooklyn College, City University of New York, New York, New York 11210, United States., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Markland TE; Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, California 94305, United States., De Fabritiis G; Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain.; Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2024 Mar 11; Vol. 64 (5), pp. 1481-1485. Date of Electronic Publication: 2024 Feb 20.

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.

Autor: Eastman P; Department of Chemistry, Stanford University, Stanford, California 94305, United States., Galvelis R; Acellera Laboratories, C Dr Trueta 183, 08005 Barcelona, Spain.; Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain., Peláez RP; Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain., Abreu CRA; Chemical Engineering Department, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 68542, Brazil.; Redesign Science Inc., 180 Varick St., New York, New York 10014, United States., Farr SE; EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom., Gallicchio E; Department of Chemistry and Biochemistry, Brooklyn College of the City University of New York, Brooklyn, New York 11210-2889, United States.; Ph.D. Program in Chemistry and Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States., Gorenko A; Stream HPC, Koningin Wilhelminaplein 1-40601, 1062 HG Amsterdam, Netherlands., Henry MM; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York New York 10065, United States., Hu F; Department of Chemistry, Stanford University, Stanford, California 94305, United States., Huang J; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China., Krämer A; Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany., Michel J; EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom., Mitchell JA; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States., Pande VS; Andreessen Horowitz, 2865 Sand Hill Rd, Menlo Park, California 94025, United States.; Department of Structural Biology, Stanford University, Stanford, California 94305, United States., Rodrigues JP; Department of Structural Biology, Stanford University, Stanford, California 94305, United States., Rodriguez-Guerra J; Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics, Virchowweg 6, 10117 Berlin, Germany., Simmonett AC; Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States., Singh S; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York New York 10065, United States., Swails J; Entos Inc., 9310 Athena Circle, La Jolla, California 92037, United States., Turner P; College of Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States., Wang Y; Simons Center for Computational Physical Chemistry and Center for Data Science, New York University, 24 Waverly Place, New York, New York 10004, United States., Zhang I; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York New York 10065, United States.; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York New York 10065, United States., De Fabritiis G; Acellera Laboratories, C Dr Trueta 183, 08005 Barcelona, Spain.; Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain.; ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain., Markland TE; Department of Chemistry, Stanford University, Stanford, California 94305, United States.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2024 Jan 11; Vol. 128 (1), pp. 109-116. Date of Electronic Publication: 2023 Dec 28.

NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics.

Autor: Galvelis R; Acellera Labs, C/Doctor Trueta 183, Barcelona 08005, Spain.; Computational Science Laboratory, Universitat Pompeu Fabra, PRBB, C/Doctor Aiguader 88, Barcelona 08003, Spain., Varela-Rial A; Acellera Ltd, Devonshire House 582 Honeypot Lane, Stanmore Middlesex, HA7 1JS, United Kingdom., Doerr S; Acellera Ltd, Devonshire House 582 Honeypot Lane, Stanmore Middlesex, HA7 1JS, United Kingdom., Fino R; Acellera Labs, C/Doctor Trueta 183, Barcelona 08005, Spain., Eastman P; Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, California 94305, United States., Markland TE; Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, California 94305, United States., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., De Fabritiis G; Computational Science Laboratory, Universitat Pompeu Fabra, PRBB, C/Doctor Aiguader 88, Barcelona 08003, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain.; Acellera Ltd, Devonshire House 582 Honeypot Lane, Stanmore Middlesex, HA7 1JS, United Kingdom.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2023 Sep 25; Vol. 63 (18), pp. 5701-5708. Date of Electronic Publication: 2023 Sep 11.

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials.

Autor: Eastman P; Department of Chemistry, Stanford University, Stanford, CA, 94305, USA. peastman@stanford.edu., Behara PK; Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA., Dotson DL; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, CA, 95616, USA., Galvelis R; Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain., Herr JE; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA., Horton JT; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom., Mao Y; Department of Chemistry, Stanford University, Stanford, CA, 94305, USA., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Pritchard BP; Molecular Sciences Software Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24060, USA., Wang Y; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.; Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA., De Fabritiis G; Acellera Labs, Doctor Trueta 183, 08005, Barcelona, Spain.; Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain and ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain., Markland TE; Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.

Publikováno v: Scientific data [Sci Data] 2023 Jan 04; Vol. 10 (1), pp. 11. Date of Electronic Publication: 2023 Jan 04.

Calculation of Some Low-Lying Electronic Excitations of Barium Monofluoride Using the Equation of Motion (EOM)-CC3 Method with an Effective Core Potential Approach.

Autor: Horbatsch, Marko¹ (AUTHOR) marko@yorku.ca

Publikováno v: Molecules. Sep2024, Vol. 29 Issue 18, p4356. 12p.