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.

Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia.

Autor: Minuesa G; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA., Albanese SK; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Xie W; Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Kazansky Y; Weill Cornell Medical College, Tri-Institutional MD-PhD Program, Rockefeller University and Sloan Kettering Institute, New York, NY, 10065, USA., Worroll D; Department of Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA., Chow A; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA., Schurer A; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA., Park SM; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA., Rotsides CZ; Chemical Biology Program, Sloan Kettering Institute and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Taggart J; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA., Rizzi A; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA., Naden LN; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Chou T; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA., Gourkanti S; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA., Cappel D; Schrödinger GmbH, Q7, 23, 68161, Mannheim, Germany., Passarelli MC; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.; Weill Cornell Medical College, Tri-Institutional MD-PhD Program, Rockefeller University and Sloan Kettering Institute, New York, NY, 10065, USA., Fairchild L; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA., Adura C; High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY, 10065, USA., Glickman JF; High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY, 10065, USA., Schulman J; Hematologic Oncology Tissue Bank, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Famulare C; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Patel M; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Eibl JK; Northern Ontario School of Medicine, Sudbury, ON, P3E 2C6, Canada., Ross GM; Northern Ontario School of Medicine, Sudbury, ON, P3E 2C6, Canada., Bhattacharya S; New York Structural Biology Center, NMR Group, New York, NY, 10027, USA., Tan DS; Chemical Biology Program, Sloan Kettering Institute and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Leslie CS; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Beuming T; Schrödinger, Inc., 120 West 45th Street, New York, NY, 10036, USA., Patel DJ; Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Goldgur Y; Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Kharas MG; Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. kharasm@mskcc.org.

Publikováno v: Nature communications [Nat Commun] 2019 Jun 19; Vol. 10 (1), pp. 2691. Date of Electronic Publication: 2019 Jun 19.

Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions.

Autor: Naden LN; Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States., Shirts MR; Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2015 Jun 09; Vol. 11 (6), pp. 2536-49.