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Affiliation(s)
- Scott R. Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
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2
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Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, United States
| | - Scott R. Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, United States
| | - Jeffrey Larson
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, United States
| | - Paul Hovland
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, United States
| | - Sven Leyffer
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, United States
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Lischka H, Shepard R, Müller T, Szalay PG, Pitzer RM, Aquino AJA, Araújo do Nascimento MM, Barbatti M, Belcher LT, Blaudeau JP, Borges I, Brozell SR, Carter EA, Das A, Gidofalvi G, González L, Hase WL, Kedziora G, Kertesz M, Kossoski F, Machado FBC, Matsika S, do Monte SA, Nachtigallová D, Nieman R, Oppel M, Parish CA, Plasser F, Spada RFK, Stahlberg EA, Ventura E, Yarkony DR, Zhang Z. The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry. J Chem Phys 2020; 152:134110. [PMID: 32268762 DOI: 10.1063/1.5144267] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.
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Affiliation(s)
- Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Thomas Müller
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich, Jülich 52428, Germany
| | - Péter G Szalay
- ELTE Eötvös Loránd University, Institute of Chemistry, Budapest, Hungary
| | - Russell M Pitzer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adelia J A Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | | | | | - Lachlan T Belcher
- Laser and Optics Research Center, Department of Physics, US Air Force Academy, Colorado 80840, USA
| | | | - Itamar Borges
- Departamento de Química, Instituto Militar de Engenharia, Rio de Janeiro, RJ 22290-270, Brazil
| | - Scott R Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Emily A Carter
- Office of the Chancellor and Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Box 951405, Los Angeles, California 90095-1405, USA
| | - Anita Das
- Indian Institute of Engineering Science and Technology, Shibpur, Howrah, India
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - William L Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Gary Kedziora
- Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Miklos Kertesz
- Department of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, DC 20057-1227, USA
| | | | - Francisco B C Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia, Pennsylvania 19122, USA
| | | | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 160610 Prague 6, Czech Republic
| | - Reed Nieman
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Markus Oppel
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Carol A Parish
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, USA
| | - Felix Plasser
- Department of Chemistry, Loughborough University, Loughborough LE11 3TU, United Kingdom
| | - Rene F K Spada
- Departamento de Física, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
| | - Eric A Stahlberg
- Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Elizete Ventura
- Universidade Federal da Paraíba, 58059-900 João Pessoa, PB, Brazil
| | - David R Yarkony
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
| | - Zhiyong Zhang
- Stanford Research Computing Center, Stanford University, 255 Panama Street, Stanford, California 94305, USA
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Shepard R, Brozell SR, Gidofalvi G. Representations of Shavitt Graphs Within the Graphical Unitary Group Approach. J Comput Chem 2020; 41:129-135. [PMID: 31602656 DOI: 10.1002/jcc.26080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/31/2019] [Indexed: 11/06/2022]
Abstract
The Shavitt graph is a visual representation of a distinct row table (DRT) within the graphical unitary group approach. The DRT is a compact representation of the entire configuration state function expansion space within a molecular electronic structure calculation. Each node of the graph is associated with an integer triple (a k ,b k ,c k ). These integers may be mapped to other quantum numbers, including the number of orbitals, number of electrons, and spin quantum number, and used to display Shavitt graphs in various ways that emphasize different aspects of the expansion space or that reveal different aspects of computed wave functions. The features of several graph density plots are discussed, including electron-hole symmetries and the bonding-antibonding wave function character. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, 60439
| | - Scott R Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, 60439
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, 502 E. Boone Ave., Spokane, Washington, 99258-0102
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Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Scott R. Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
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Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem 2015; 36:1132-56. [PMID: 25914306 DOI: 10.1002/jcc.23905] [Citation(s) in RCA: 429] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 03/01/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, 11794
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Abstract
Four representations and parametrizations of orthogonal matrices Q ∈ R(m×n) in terms of the minimal number of essential parameters {φ} are discussed: the exponential representation, the Householder reflector representation, the Givens rotation representation, and the rational Cayley transform representation. Both square n = m and rectangular n < m situations are considered. Two separate kinds of parametrizations are considered: one in which the individual columns of Q are distinct, the Stiefel manifold, and the other in which only span(Q) is significant, the Grassmann manifold. The practical issues of numerical stability, continuity, and uniqueness are discussed. The computation of Q in terms of the essential parameters {φ}, and also the extraction of {φ} for a given Q are considered for all of the parametrizations. The transformation of gradient arrays between the Q and {φ} variables is discussed for all representations. It is our hope that developers of new methods will benefit from this comparative presentation of an important but rarely analyzed subject.
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Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
| | - Scott R Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
| | - Gergely Gidofalvi
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
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Shepard R, Gidofalvi G, Brozell SR. The multifacet graphically contracted function method. I. Formulation and implementation. J Chem Phys 2014; 141:064105. [DOI: 10.1063/1.4890734] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, 502 E. Boone Ave., Spokane, Washington 99258-0102, USA
| | - Scott R. Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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Shepard R, Gidofalvi G, Brozell SR. The multifacet graphically contracted function method. II. A general procedure for the parameterization of orthogonal matrices and its application to arc factors. J Chem Phys 2014; 141:064106. [DOI: 10.1063/1.4890735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, 502 E. Boone Ave., Spokane, Washington 99258-0102, USA
| | - Scott R. Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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Affiliation(s)
- Scott R. Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439
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Beck EV, Brozell SR, Blaudeau JP, Burggraf LW, Pitzer RM. Assessment of the Accuracy of Shape-Consistent Relativistic Effective Core Potentials Using Multireference Spin−Orbit Configuration Interaction Singles and Doubles Calculations of the Ground and Low-Lying Excited States of U4+ and U5+. J Phys Chem A 2009; 113:12626-31. [DOI: 10.1021/jp9049846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric V. Beck
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-159, Livermore, California 94551, Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, Ohio 43212, High Performance Technologies Incorporated, U.S. Army Research Laboratory, Building 394, Aberdeen Proving Ground, Maryland 21005, Department of Engineering Physics, Air Force Institute of Technology, AFIT/ENP, 2950 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433, and Department of Chemistry, The Ohio State University, 100 West 18th
| | - Scott R. Brozell
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-159, Livermore, California 94551, Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, Ohio 43212, High Performance Technologies Incorporated, U.S. Army Research Laboratory, Building 394, Aberdeen Proving Ground, Maryland 21005, Department of Engineering Physics, Air Force Institute of Technology, AFIT/ENP, 2950 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433, and Department of Chemistry, The Ohio State University, 100 West 18th
| | - Jean-Philippe Blaudeau
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-159, Livermore, California 94551, Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, Ohio 43212, High Performance Technologies Incorporated, U.S. Army Research Laboratory, Building 394, Aberdeen Proving Ground, Maryland 21005, Department of Engineering Physics, Air Force Institute of Technology, AFIT/ENP, 2950 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433, and Department of Chemistry, The Ohio State University, 100 West 18th
| | - Larry W. Burggraf
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-159, Livermore, California 94551, Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, Ohio 43212, High Performance Technologies Incorporated, U.S. Army Research Laboratory, Building 394, Aberdeen Proving Ground, Maryland 21005, Department of Engineering Physics, Air Force Institute of Technology, AFIT/ENP, 2950 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433, and Department of Chemistry, The Ohio State University, 100 West 18th
| | - Russell M. Pitzer
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-159, Livermore, California 94551, Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, Ohio 43212, High Performance Technologies Incorporated, U.S. Army Research Laboratory, Building 394, Aberdeen Proving Ground, Maryland 21005, Department of Engineering Physics, Air Force Institute of Technology, AFIT/ENP, 2950 Hobson Way, Wright-Patterson Air Force Base, Ohio 45433, and Department of Chemistry, The Ohio State University, 100 West 18th
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Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. DOCK 6: combining techniques to model RNA-small molecule complexes. RNA 2009; 15:1219-30. [PMID: 19369428 PMCID: PMC2685511 DOI: 10.1261/rna.1563609] [Citation(s) in RCA: 542] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there is a need for the tools used in protein-based drug design, particularly DOCKing algorithms, to be extended or adapted for nucleic acids. Here, we have compiled a test set of RNA-ligand complexes to validate the ability of the DOCK suite of programs to successfully recreate experimentally determined binding poses. With the optimized parameters and a minimal scoring function, 70% of the test set with less than seven rotatable ligand bonds and 26% of the test set with less than 13 rotatable bonds can be successfully recreated within 2 A heavy-atom RMSD. When DOCKed conformations are rescored with the implicit solvent models AMBER generalized Born with solvent-accessible surface area (GB/SA) and Poisson-Boltzmann with solvent-accessible surface area (PB/SA) in combination with explicit water molecules and sodium counterions, the success rate increases to 80% with PB/SA for less than seven rotatable bonds and 58% with AMBER GB/SA and 47% with PB/SA for less than 13 rotatable bonds. These results indicate that DOCK can indeed be useful for structure-based drug design aimed at RNA. Our studies also suggest that RNA-directed ligands often differ from typical protein-ligand complexes in their electrostatic properties, but these differences can be accommodated through the choice of potential function. In addition, in the course of the study, we explore a variety of newly added DOCK functions, demonstrating the ease with which new functions can be added to address new scientific questions.
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Affiliation(s)
- P Therese Lang
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94143, USA
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Naleway C, Seth M, Shepard R, Wagner AF, Tilson JL, Ermler WC, Brozell SR. An ab initio study of the ionization potentials and f–f spectroscopy of europium atoms and ions. J Chem Phys 2002. [DOI: 10.1063/1.1455619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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