NAMD: A case study in multilingual parallel programming

Kalé, Laxmikant V.; Bhandarkar, Milind; Brunner, Richard; Krawetz, N.; Philips, J.; Shinozaki, Aritomo

doi:10.1007/bfb0032705

Cited by 17 publications

(4 citation statements)

References 8 publications

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“…49 RAMD MD Simulations. In order to figure out possible channels for the substrate delivery to the active site, the combined random acceleration molecular dynamics and MD simulations (RAMD-MD) have been carried out by using NAMD 2.9, 55 which has been successfully used in previous theoretical studies. 56−59 In the RAMD-MD simulations, an additional force with the random orientation was added to the center of mass for the ligand to identify the possible pathways for the ligand fleeing away from the protein within a certain period of time.…”

Section: Methodsmentioning

confidence: 99%

A Comprehensive Understanding of Enzymatic Degradation of the G-Type Nerve Agent by Phosphotriesterase: Revised Role of Water Molecules and Rate-Limiting Product Release

Fan

Zheng²,

Zhang

et al. 2019

ACS Catal.

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Nerve agents are highly toxic organophosphorus compounds, and the wild-type phosphotriesterase (PTE) enzyme is capable of hydrolyzing these organophosphates but with a low catalytic efficiency. Here the whole enzymatic detoxification process of the G-type nerve agent sarin by the PTE enzyme, including the substrate delivery, the chemical reaction, and the product release, has been explored by extensive QM/MM MD and MM MD simulations. The plausible mechanisms for the chemical and nonchemical steps, the roles of water molecules, and the key residues have been discussed. The enzymatic P–F cleavage of sarin is a two-step exothermic process with the free-energy span of 12.3 kcal/mol, and it should be facile in the whole enzymatic catalysis. On the contrary, the initial degraded product is tightly bound to the binuclear zinc center, and its dissociation experiences multiple chemical steps with the free-energy barriers of 21.0 kcal/mol for the recombination process and 18.3 kcal/mol for the release of the product phosphoester from the active site. Notably, the solvation of hydrophilic products in the bulk water is generally exothermic, which provides the driving force for the release of products from the active site. The side-chain residues Leu271 and Phe132 in the transportation channel function as the entrance gate in PTE and play an important gate-switching role to manipulate the substrate access to the active site and the product release. These mechanistic details for the enzymatic degradation of sarin by PTE provide significant clues to improve its activity toward the nerve agents.

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Section: Methodsmentioning

confidence: 99%

A Comprehensive Understanding of Enzymatic Degradation of the G-Type Nerve Agent by Phosphotriesterase: Revised Role of Water Molecules and Rate-Limiting Product Release

Fan

Zheng²,

Zhang

et al. 2019

ACS Catal.

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“…All simulated system were molecular dynamic simulated within the NAMD 2.9 program (Kalé et al 1997) using CHARMM36 force eld (Brooks et al 2012) parameters. Before obtaining the nal MD trajectory, systems were energy minimized in NVT ensemble using the following parameters: time step of 2 fs; cutoff: 12 Å for describing short-range interactions as well as particle-mesh Ewald (PME) formalism was…”

Section: Molecular Dynamic Simulationmentioning

confidence: 99%

Bacterial cellulose-based scaffold: synthesis and surface modification for sustained rifampicin release for topic skin infections treatment

Yamada,

Lazarini,

do Amaral

et al. 2024

Cellulose

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The present work aims the production of bacterial cellulose (BC), by Komagataeibacter hansenii, and the surface modi cations by methanol treatment to produce membranes with different physical characteristics that allow the use of device for sustained release of the antibacterial drug rifampicin (RIF) with broad spectrum and bactericidal activity against Gram-positive and Gram-negative species, being able to penetrate bacterial bio lms, for potential use as a dressing for the prevention or treatment of SSTIs. Here, BC produced was treated with methanol (BC-MetOH) to obtain optimized membranes for use as sustained release devices for the antibacterial RIF. The parameters evaluated were ber densities, thickness, and entanglement of BC-MetOH impregnated by RIF in methanolic solution (BC-MetOH-RIF) compared to BC-dH 2 O impregnated by RIF in aqueous solution (BC-dH 2 O-RIF) in regarding the capacity for sustained release of RIF. BC-MetOH-RIF and BC-dH 2 O-RIF were characterized by eld emission scanning electron microscopy (FEG-SEM), thermogravimetric analysis, and Fourier transform infrared spectroscopy. The comparison between the sustained release capacity of RIF by BC-RIF-MetOH and BC-RIF-dH 2 O were analyzed by disc diffusion technique. Intermolecular interactions between RIF and BC were accounted for in water and methanol solutions using molecular dynamics (MD) simulations. Both FEG-SEM and MD simulations demonstrated that the interaction energy of the BC-RIF-MetOH set related to the RIF-BC is stronger in methanol solution than in water. The results obtained demonstrate that BC-RIF-MetOH can contribute to the increase of the therapeutic arsenal for bacterial infections treatment of the SSTIs.

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“…It performs molecular energy simulations, real-time monitoring, communication among participants, and document management. BioCore can also combined with existing software tools such as VMD [ 10 ] (a visualization tool) and NAMD [ 11 ] (a computational system). However, BioCore strictly requires a high performance PC for effective and efficient exercises of collaborations, and the network system of BioCore is not an open standard.…”

Section: Related Workmentioning

confidence: 99%

A Collaborative Molecular Modeling Environment Using a Virtual Tunneling Service

Lee

Kim

Kang

2012

Journal of Biomedicine and Biotechnology

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Collaborative researches of three-dimensional molecular modeling can be limited by different time zones and locations. A networked virtual environment can be utilized to overcome the problem caused by the temporal and spatial differences. However, traditional approaches did not sufficiently consider integration of different computing environments, which were characterized by types of applications, roles of users, and so on. We propose a collaborative molecular modeling environment to integrate different molecule modeling systems using a virtual tunneling service. We integrated Co-Coot, which is a collaborative crystallographic object-oriented toolkit, with VRMMS, which is a virtual reality molecular modeling system, through a collaborative tunneling system. The proposed system showed reliable quantitative and qualitative results through pilot experiments.

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NAMD: A case study in multilingual parallel programming

Cited by 17 publications

References 8 publications

A Comprehensive Understanding of Enzymatic Degradation of the G-Type Nerve Agent by Phosphotriesterase: Revised Role of Water Molecules and Rate-Limiting Product Release

A Comprehensive Understanding of Enzymatic Degradation of the G-Type Nerve Agent by Phosphotriesterase: Revised Role of Water Molecules and Rate-Limiting Product Release

Bacterial cellulose-based scaffold: synthesis and surface modification for sustained rifampicin release for topic skin infections treatment

A Collaborative Molecular Modeling Environment Using a Virtual Tunneling Service

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