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Gubbins KE, Moore JD. Molecular Modeling of Matter: Impact and Prospects in Engineering. Ind Eng Chem Res 2010. [DOI: 10.1021/ie901909c] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Keith E. Gubbins
- Institute for Computational Science & Engineering and Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Joshua D. Moore
- Institute for Computational Science & Engineering and Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
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High Performance Computing in Computational Chemistry: Methods and Machines. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125830.ch4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Sanbonmatsu KY, Tung CS. High performance computing in biology: multimillion atom simulations of nanoscale systems. J Struct Biol 2006; 157:470-80. [PMID: 17187988 PMCID: PMC1868470 DOI: 10.1016/j.jsb.2006.10.023] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Revised: 09/05/2006] [Accepted: 10/03/2006] [Indexed: 11/16/2022]
Abstract
Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nano-scale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail.
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Affiliation(s)
- K Y Sanbonmatsu
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, MS K710, Los Alamos, NM 87545, USA.
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Hermida-Ramón JM, Karlström G, Lindh R. Analysis of the Relative Stability of cis-Urocanic Acid in Condensed Phase. The Use of Langevin Dipoles. J Phys Chem B 2002. [DOI: 10.1021/jp025893r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jose Manuel Hermida-Ramón
- Department of Theoretical Chemistry and Department of Chemical Physics, Chemical Center, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
| | - Gunnar Karlström
- Department of Theoretical Chemistry and Department of Chemical Physics, Chemical Center, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
| | - Roland Lindh
- Department of Theoretical Chemistry and Department of Chemical Physics, Chemical Center, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
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Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000; 100:4187-4226. [PMID: 11749344 DOI: 10.1021/cr990052a] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, E-08028 Barcelona, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, E-08028 Barcelona, Spain
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Roccatano D, Bizzarri R, Chillemi G, Sanna N, Di Nola A. Development of a parallel molecular dynamics code on SIMD computers: Algorithm for use of pair list criterion. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(199805)19:7<685::aid-jcc1>3.0.co;2-m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Grubmüller H, Heymann B, Tavan P. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996; 271:997-9. [PMID: 8584939 DOI: 10.1126/science.271.5251.997] [Citation(s) in RCA: 620] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The force required to rupture the streptavidin-biotin complex was calculated here by computer simulations. The computed force agrees well with that obtained by recent single molecule atomic force microscope experiments. These simulations suggest a detailed multiple-pathway rupture mechanism involving five major unbinding steps. Binding forces and specificity are attributed to a hydrogen bond network between the biotin ligand and residues within the binding pocket of streptavidin. During rupture, additional water bridges substantially enhance the stability of the complex and even dominate the binding interactions. In contrast, steric restraints do not appear to contribute to the binding forces, although conformational motions were observed.
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Affiliation(s)
- H Grubmüller
- Theoretische Biophysik, Institut für Medizinische Optik, Ludwig- Maximilians-Universität München, Germany. Helmut.Grubmueller@ Physik.uni-muenchen.de
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Schaefer M, Karplus M. A Comprehensive Analytical Treatment of Continuum Electrostatics. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp9521621] [Citation(s) in RCA: 468] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Schaefer
- Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Université Louis Pasteur, 4, rue Blaise Pascal, 67000 Strasbourg, France
| | - Martin Karplus
- Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Université Louis Pasteur, 4, rue Blaise Pascal, 67000 Strasbourg, France
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Abstract
Molecular dynamics simulations have been conducted to investigate the binding of the glucocorticoid receptor (GR) dimer to DNA. For this purpose simulations of the complex formed by a DNA segment and a dimer of GR-DNA binding domains (GR-DBD) have been carried out, employing an available X-ray structure. A second set of simulations was based on this structure as well, except that the DNA segment was altered to the consensus glucocorticoid response element (GRE). Simulations of a single GR-DBD and of the uncomplexed GRE served as controls. For the simulations, each system was encapsulated in an ellipsoid of water. Protein-DNA interactions, dimer interactions, and DNA structural parameters were analyzed for each system and compared. The consensus GRE is found to yield more favorable and symmetric interactions between the GR-DBDs and the GRE, explaining the ability of the GR dimer to recognize this DNA segment. Further analysis focused on deformations of the DNA that are induced by the binding of GR. The deformations observed involve a 35 degree bend of the DNA, an unwinding, and a displacement of the helical axis. These deformations are consistent with a mechanism for transcriptional regulation that involves a change of nucleosome packing upon GR binding. Significant protein-protein and protein-DNA interactions, both direct and water mediated, develop due to the deformations of the GRE and are indicative of an increased recognition achieved through DNA deformation. The interactions include direct interactions between the GRE and glycine-458 and serine-459, side groups which differentiate GR from other members of the nuclear hormone receptor family.
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Affiliation(s)
- T C Bishop
- Beckman Institute, Department of Chemistry, University of Illinois at Urbana-Champaign 61801, USA
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Grubmüller H, Tavan P. Molecular dynamics of conformational substates for a simplified protein model. J Chem Phys 1994. [DOI: 10.1063/1.467427] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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McGarrah D, Judson R. Analysis of the genetic algorithm method of molecular conformation determination. J Comput Chem 1993. [DOI: 10.1002/jcc.540141115] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Lin S, Mellor-Crummey J, Pettitt B, Phillips G. Molecular dynamics on a distributed-memory multiprocessor. J Comput Chem 1992. [DOI: 10.1002/jcc.540130813] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Shifman MA, Windemuth A, Schulten K, Miller PL. Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language. COMPUTERS AND BIOMEDICAL RESEARCH, AN INTERNATIONAL JOURNAL 1992; 25:168-80. [PMID: 1582193 DOI: 10.1016/0010-4809(92)90019-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper reviews these approaches and develops a straightforward but effective algorithm using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.
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Affiliation(s)
- M A Shifman
- Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut 06510
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Coupling of protein motion to electron transfer: Molecular dynamics and stochastic quantum mechanics study of photosynthetic reaction centers. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)87081-6] [Citation(s) in RCA: 128] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Grubmüller H, Heller H, Windemuth A, Schulten K. Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions. MOLECULAR SIMULATION 1991. [DOI: 10.1080/08927029108022142] [Citation(s) in RCA: 215] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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