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Molecular Dynamics Inc amber program package
Amber Program 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/amber+program+package/package+program/pmc13009001-49-27-3
Average 86 stars, based on 1 article reviews
amber program package - by Bioz Stars, 2026-09
86/100 stars

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Article Title: DNA mutation motifs in the genes associated with inherited diseases
Article Snippet: In particular, we employed Molecular Dynamics (MD) simulations implemented in the AMBER program package [ ] and free energy calculations using the adaptive biasing method (ABF) [ ] enhanced by the multiple walker approach (MWA) [ ].

Article Title: Transport Dynamics of Water Molecules Confined between Lipid Membranes.
Article Snippet: 14 S2 Table of contents 15 16 Supplementary Text S1: Computational details of molecular dynamics simulations .. S3 17 Supplementary Text S2: Derivation of analytic expressions for the MSD and NGP ... S6 18 Figure S1: z-dependent profiles of lateral diffusion coefficient ................................. S11 19 Figure S2: z-dependent profiles of longitudinal diffusion coefficient ....................... S15 20 Figure S3: Diffusion Kernel Correlation and Non-Gaussian Parameter .................... S17 21 Figure S4: Relationship between DKC and NGP at long times ................................. S20 22 Caption for Movie S1: Heatmap of discrete Green’s function ................................... S21 23 Tables S1-S4 ............................................................................................................... S23 24 Supplementary References ......................................................................................... S26 25 26 27 S3 Supplementary Text S1: Computational details of molecular dynamics 28 simulations 29 Molecular Dynamics (MD) simulations were carried out using the AMBER 21 program 30 package.

Article Title: Different Structures-Similar Effect: Do Substituted 5-(4-Methoxyphenyl)-1 H -indoles and 5-(4-Methoxyphenyl)-1 H -imidazoles Represent a Common Pharmacophore for Substrate Selective Inhibition of Linoleate Oxygenase Activity of ALOX15?
Article Snippet: Molecular Dynamics Simulations The recommended procedure by the AMBER program package [51] was used to assemble all systems.

Modification:

Article Title: Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme.
Article Snippet: It is known that bacteria contain inhibitors of lysozyme activity.. The recently discovered Escherichia coli inhibitor of vertebrate lysozyme (Ivy) and its potential interactions with several goose-type (g-type) lysozymes from fish were studied using functional enzyme assays, comparative homology modelling, protein–protein docking, and molecular dynamics simulations.. Enzyme assays carried out on salmon g-type lysozyme revealed a lack of inhibition by Ivy.

Binding Assay:

Article Title: Virtual screening of compounds for the development of thyroid hormone analogues for potential application in cardiac regeneration
Article Snippet: .. Continuing the screening, Molecular Dynamics simulations were performed with NAMD program ( ) and Free Energy of Binding by Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) were calculated with AMBER program package ( ) (details in Sect. and ), semiempirical Quantum Mechanics, PM7 , and hybrid Quantum Mechanics Molecular Mechanics (QMMM) (B3LYP 6-31G*/CHARMM36) were calculated with Orca 5 software ( ) (details in 2.9 Quantum Mechanics Molecular Mechanics Hybrid Calculation). ..

Software:

Article Title: Virtual screening of compounds for the development of thyroid hormone analogues for potential application in cardiac regeneration
Article Snippet: .. Continuing the screening, Molecular Dynamics simulations were performed with NAMD program ( ) and Free Energy of Binding by Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) were calculated with AMBER program package ( ) (details in Sect. and ), semiempirical Quantum Mechanics, PM7 , and hybrid Quantum Mechanics Molecular Mechanics (QMMM) (B3LYP 6-31G*/CHARMM36) were calculated with Orca 5 software ( ) (details in 2.9 Quantum Mechanics Molecular Mechanics Hybrid Calculation). ..



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