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Molecular Dynamics Inc namd 2 13 molecular dynamics software package
Namd 2 13 Molecular Dynamics Software Package, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/namd+molecular+dynamics+package/namd+software/pmc12564135-254-7-11
Average 86 stars, based on 1 article reviews
namd 2 13 molecular dynamics software package - by Bioz Stars, 2026-10
86/100 stars

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Article Title: AT-hook peptides bind the major and minor groove of AT-rich DNA duplexes
Article Snippet: The modeled DNA hairpin structure was optimized by energy minimization with CHARMM36 force field ( ) using NAMD Molecular Dynamics package ( ).

Article Title: Transcriptome analysis of Corvus splendens reveals a repertoire of antimicrobial peptides
Article Snippet: Molecular dynamics was carried out on this system using the NAMD molecular dynamics package and the CHARMM36 force field .

Article Title: AT-hook peptides bind the major and minor groove of AT-rich DNA duplexes.
Article Snippet: The modeled DNA hairpin structure was optimized by energy minimization with CHARMM36 force field (34) using NAMD Molecular Dynamics package (35).

Article Title: ATP-Dependent Signaling in Simulations of a Revised Model of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).
Article Snippet: Cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the ATP-binding cassette (ABC) transporter superfamily that has uniquely evolved to function as a chloride channel.. It binds and hydrolyzes ATP at its nucleotide binding domains to form a pore providing a diffusive pathway within its transmembrane domains.. CFTR is the only known protein from the ABC superfamily with channel activity, and its dysfunction causes the disease cystic fibrosis.

Article Title: Transcriptome analysis of Corvus splendens reveals a repertoire of antimicrobial peptides.
Article Snippet: Molecular dynamics was carried out on this system using the NAMD molecular dynamics package127 and the CHARMM36 force field128.

Article Title: Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates
Article Snippet: The simulations were performed using the NAMD molecular dynamics package with an electrostatic cutoff of 12 Å units and a van der Waals cutoff of 10 Å units along with periodic boundary conditions.

Article Title: Exploring the Effects of Dopamine and DMMP Additives on Improving the Cycle Boosting and Nonflammability of Electrolytes in Full-Cell Lithium-Ion Batteries (18650)
Article Snippet: The dcd trajectories as obtained from NAMD molecular dynamics package were converted to trr files compatible with gromacs tool using Visual Molecular Dynamics software.

Generated:

Article Title: Structure and Mechanism of a Cold-Adapted Bacterial Lipase
Article Snippet: .. All MD simulations were run using the NAMD molecular dynamics package, the CHARMM36 protein force field and the TIP3P water model. Parameters for the 4-nitrophenol butyrate and ester side chain were generated using cGenFF. ..



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