M. Nelson et al., "MDScope: A Visual Computing Environment for Structural Biology," Computer Physics Comm., Vol. 91, 1995, pp. 111-134. Home/Search Document Not in Database Summary Related Articles Check |
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Quantum Chemical Modeling of Co-C bond activation in B-12.. - Kozlowski (2002) (18 citations) Self-citation (Gursoy Kale Skeel Schulten) (Correct)
....or dihedrals to which additional restraining forces should be applied. These restraints are monitored and modified during the course of the simulation to calculate the free energy di#erence between two configurations of the molecule. 5.3. 4 MDScope: Interactive Modeling with VMD In MDScope 2 [31] NAMD2 is connected to the molecular visualization package VMD 3 [18] allowing the user to view a remotely running simulation and to apply forces to atoms, residues, or molecules. All atoms of the simulation are sent to VMD using the same coordinate collection methods used for trajectory ....
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope -- A visual computing environment for structural biology. In S.N. Atluri, G. Yagawa, and T.A. Cruse, editors, Computational Mechanics 95, volume 1, pages 476--481, 1995.
Quantum Chemical Modeling of Co-C bond activation in B-12.. - Kozlowski (2002) (18 citations) Self-citation (Gursoy Kale Skeel Schulten) (Correct)
....use periodic boundary conditions over any combination of the three coordinate axes. It performs cuto# simulations or full electrostatic simulations employing multiple timestepping using the DPMTA [40] or DPME [46] libraries. NAMD2 can connect to VMD [18] the visualization component of MDSCOPE [30] to allow monitoring of and interaction with ongoing simulations. We will first describe the core structure of NAMD2. The specific algorithms and interesting data structures used for force computations are described next. To make a modular implementation of NAMD2 possible, it was necessary to ....
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope -- a visual computing environment for structural biology. Comput. Phys. Commun., 91(1, 2 and 3):111--134, 1995.
BioCoRE: A Collaboratory for Structural Biology - Bhandarkar, Budescu.. (1999) Self-citation (Humphrey Schulten) (Correct)
....development of BioCoRE is based on successful efforts in advanced software, novel algorithms and state of the art hardware. The software developed is freely available to the biomedical community and is widely distributed. We have taken a broad approach, reflected in the modeling package MDScope (Nelson et al. 1995) which includes our popular molecular graphics program VMD (Humphrey et al. 1996) Efforts have also been invested to apply parallel computer architectures for molecular dynamics simulations. To this end the program NAMD y (Nelson et al. 1996; Kal e et al. 1997; Kale et al. 1998; Kal e et ....
Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kal'e, L., Skeel, R., Schulten, K., and Kufrin, R. 1995. MDScope -- A Visual Computing Environment for Structural Biology. Comput. Phys.
SMD: Visual Steering of - Molecular Dynamics For (Correct)
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M. Nelson et al., "MDScope: A Visual Computing Environment for Structural Biology," Computer Physics Comm., Vol. 91, 1995, pp. 111-134.
SMD: Visual Steering of Molecular Dynamics for Protein Design - Leech (1996) (6 citations) (Correct)
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M. Nelson et al., "MDScope: A Visual Computing Environment for Structural Biology," Computer Physics Comm., Vol. 91, 1995, pp. 111-134.
A Virtual Environment for Steered Molecular Dynamics - Prins, Hermans, Mann.. (1999) (Correct)
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M. Nelson et al., "MDScope: A visual computing environment for structural biology", Comput. Phys. Comm. 91:111-134, 1995.
Parallel MD-Simulations of Synthetic Polymers - Jung, Lenhof, Müller.. (1997) (Correct)
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M. Nelson, W. Humprey, A. Gursory, A. Dalke, L. Kale, R. Skeel, K. Schulten, R. Kufrin : "MD--Scope: A Visual Computing Environment for Structural Biology". Computational Physics Communications 91, 1995, pp. 111--134.
Parallel Algorithms for MD-Simulations of Synthetic Polymers - Jung, Lenhof, Müller, Rüb (1997) (Correct)
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M. Nelson, W. Humprey, A. Gursory, A. Dalke, L. Kale, R. Skeel, K. Schulten, R. Kufrin : "MD--Scope: A Visual Computing Environment for Structural Biology". Computational Physics Communications 91, 1995, pp. 111--134.
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