Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields.

Autor: Behara PK; Center for Neurotherapeutics, University of California, Irvine, California 92697, United States., Jang H; Chemistry Department, University of California at Davis, Davis, California 95616, United States.; OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States., Horton JT; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K., Gokey T; Department of Chemistry, University of California, Irvine, California 92697, United States., Dotson DL; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States.; Datryllic LLC, Phoenix, Arizona 85003, United States., Boothroyd S; Boothroyd Scientific Consulting Ltd., London WC2H 9JQ, U.K., Bayly CI; OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States., Cole DJ; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K., Wang LP; Chemistry Department, University of California at Davis, Davis, California 95616, United States., Mobley DL; Center for Neurotherapeutics, University of California, Irvine, California 92697, United States.; Department of Chemistry, University of California, Irvine, California 92697, United States.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2024 Aug 15; Vol. 128 (32), pp. 7888-7902. Date of Electronic Publication: 2024 Aug 01.

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.

Autor: Boothroyd S; Boothroyd Scientific Consulting Ltd., London WC2H 9JQ, U.K., Behara PK; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States., Madin OC; Chemical & Biological Engineering Department, University of Colorado Boulder, Boulder, Colorado 80309, United States., Hahn DF; Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium., Jang H; Chemistry Department, The University of California at Davis, Davis, California 95616, United States.; OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States., Gapsys V; Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium.; Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany., Wagner JR; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States., Horton JT; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K., Dotson DL; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States.; Datryllic LLC, Phoenix, Arizona 85003, United States., Thompson MW; Chemical & Biological Engineering Department, University of Colorado Boulder, Boulder, Colorado 80309, United States.; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States., Maat J; Department of Chemistry, University of California, Irvine, California 92697, United States., Gokey T; Department of Chemistry, University of California, Irvine, California 92697, United States., Wang LP; Chemistry Department, The University of California at Davis, Davis, California 95616, United States., Cole DJ; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K., Gilson MK; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States., Chodera JD; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Bayly CI; OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States., Shirts MR; Chemical & Biological Engineering Department, University of Colorado Boulder, Boulder, Colorado 80309, United States., Mobley DL; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.; Department of Chemistry, University of California, Irvine, California 92697, United States.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2023 Jun 13; Vol. 19 (11), pp. 3251-3275. Date of Electronic Publication: 2023 May 11.

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.

Autor: D'Amore L; Computational Chemistry, Janssen R&D, C/Jarama 75A, 45007Toledo, Spain., Hahn DF; Computational Chemistry, Janssen R&D, Turnhoutseweg 30, BeerseB-2340, Belgium., Dotson DL; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California95616, United States., Horton JT; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon TyneNE1 7RU, U.K., Anwar J; Department of Chemistry, Lancaster University, LancasterLA1 4YW, U.K., Craig I; Molecular Modeling & Drug Discovery, BASF SE, 67056Ludwigshafen, Germany., Fox T; Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397Biberach/Riss, Germany., Gobbi A; Genentech, Inc., 1 DNA Way, South San Francisco, California94080, United States., Lakkaraju SK; Small Molecule Drug Discovery, Bristol Myers Squibb, Princeton, New Jersey08540, United States., Lucas X; Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070Basel, Switzerland., Meier K; Computational Life Science Technology Functions, Crop Science, R&D, Bayer AG, 40789Monheim, Germany., Mobley DL; Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine92617, United States., Narayanan A; Data and Computational Sciences, Vertex Pharmaceuticals, 50 Northern Avenue, Boston, Massachusetts02210, United States., Schindler CEM; Computational Chemistry & Biologics, Merck KGaA, Frankfurter Strasse 250, 64293Darmstadt, Germany., Swope WC; Genentech, Inc., 1 DNA Way, South San Francisco, California94080, United States., In 't Veld PJ; Molecular Modeling & Drug Discovery, BASF SE, 67056Ludwigshafen, Germany., Wagner J; The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California95616, United States.; Chemistry Department, The University of California at Irvine, Irvine, California92617, United States., Xue B; XtalPi Inc. Floor 3, International Biomedical Innovation Park II, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, Guangdong518040, China., Tresadern G; Computational Chemistry, Janssen R&D, Turnhoutseweg 30, BeerseB-2340, Belgium.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2022 Dec 12; Vol. 62 (23), pp. 6094-6104. Date of Electronic Publication: 2022 Nov 26.

Exploration and validation of force field design protocols through QM-to-MM mapping.

Autor: Ringrose C; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK. daniel.cole@ncl.ac.uk., Horton JT; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK. daniel.cole@ncl.ac.uk., Wang LP; Department of Chemistry, The University of California at Davis, Davis, California 95616, USA., Cole DJ; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK. daniel.cole@ncl.ac.uk.

Publikováno v: Physical chemistry chemical physics : PCCP [Phys Chem Chem Phys] 2022 Jul 21; Vol. 24 (28), pp. 17014-17027. Date of Electronic Publication: 2022 Jul 21.

Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Autor: Smith DGA; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Lolinco AT; Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA., Glick ZL; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Lee J; Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA., Alenaizan A; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Barnes TA; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Borca CH; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Di Remigio R; Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway., Dotson DL; Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA., Ehlert S; Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany., Heide AG; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Herbst MF; Applied and Computational Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany., Hermann J; FU Berlin, Department of Mathematics and Computer Science, 14195 Berlin, Germany., Hicks CB; Department of Chemistry, Stanford University, Stanford, California 94305, USA., Horton JT; Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom., Hurtado AG; Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-5250, USA., Kraus P; School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth 6845, WA, Australia., Kruse H; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic., Lee SJR; California Institute of Technology, Pasadena, California 91125, USA., Misiewicz JP; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Naden LN; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Ramezanghorbani F; Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA., Scheurer M; Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany., Schriber JB; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Simmonett AC; Laboratory of Computational Biology, National Institutes of Health-National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA., Steinmetzer J; Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany., Wagner JR; Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA., Ward L; Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA., Welborn M; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Altarawy D; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Anwar J; Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA., Dreuw A; Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany., Kulik HJ; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA., Liu F; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA., Martínez TJ; Department of Chemistry, Stanford University, Stanford, California 94305, USA., Matthews DA; The Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, USA., Schaefer HF 3rd; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Šponer J; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic., Turney JM; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Wang LP; Department of Chemistry, University of California Davis, Davis, California 95616, USA., De Silva N; Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA., King RA; Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, USA., Stanton JF; Quantum Theory Project, The University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, USA., Gordon MS; Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA., Windus TL; Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA., Sherrill CD; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Burns LA; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2021 Nov 28; Vol. 155 (20), pp. 204801.