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Molecular Dynamics Inc pmemd engine
Pmemd Engine, 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/pmemd+engine/engine+pmemd/pm41219307-153-12-0
Average 86 stars, based on 1 article reviews
pmemd engine - by Bioz Stars, 2026-10
86/100 stars

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Article Title: Unveiling potential Helicobacter pylori vaccine candidates: A comprehensive multi-epitope approach.
Article Snippet: Helicobacter pylori is a pathogen known to cause persistent inflammation, leading to a wide spectrum of gastrointestinal diseases and gastric lesions.. The chronic nature of this infection critically depends on host immune recognition and antigen presentation mechanisms, particularly those mediated by the major histocompatibility complex (MHC), a cluster of genes encoding cell-surfaces proteins that enable the immune system to detect and respond to foreign antigens.. In this study, computational approaches were employed to identify and evaluate potential H. pylori targets for vaccine development, with a particular focus on antigenic and immunogenic epitopes associated with MHC class I and II molecules.

Article Title: Modelling Osteoporosis in Pre-Clinical Research-Challenges, Trends and New Approaches.
Article Snippet: Mouse RANKL was simulated based on crystal structure from the protein data bank, using the CUDA version of PMEMD (Particle Mesh Ewald Molecular Dynamics).

Article Title: Overriding Traditional Electronic Effects in Biocatalytic Baeyer-Villiger Reactions by Directed Evolution
Article Snippet: Molecular Dynamics simulations were performed using the GPU code (pmemd) 14 of the AMBER 16 package.

Article Title: Modelling Osteoporosis in Pre-Clinical Research—Challenges, Trends and New Approaches
Article Snippet: Mouse RANKL was simulated based on crystal structure from the protein data bank, using the CUDA version of PMEMD (Particle Mesh Ewald Molecular Dynamics).

Article Title: Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.
Article Snippet: Molecular dynamics simulations were performed using the CUDA version of AMBER24 [38] with PMEMD, employing the ff19SB force field [39] for the protein and the gaff2 force field [40] for the ligand.

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Article Title: Targeting cancer and SARS-CoV-2: phytochemical, biological and molecular dynamic investigations of Sargassum aquifolium and Galaxaura rugosa
Article Snippet: .. Molecular Dynamics (MD) simulations were conducted utilizing the GPU version of the PMEMD engine included in the AMBER 18 software package . ..

Article Title: Targeting cancer and SARS-CoV-2: phytochemical, biological and molecular dynamic investigations of Sargassum aquifolium and Galaxaura rugosa.
Article Snippet: .. Molecular Dynamics (MD) simulations were conducted utilizing the GPU version of the PMEMD engine included in the AMBER 18 software package48. ..

Article Title: Identification and mechanistic insights into immunomodulatory peptides from soft-shelled turtle hydrolysates.
Article Snippet: The soft-shelled turtle (Pelodiscus sinensis) is prized for its nutritional and medicinal properties and represents an excellent source of bioactive peptides.. This study elucidates the immunomodulatory mechanisms of peptides from soft-shelled turtle.. Peptide sequences were virtually screened against Toll-like receptors targets, including TLR4/MD2.



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