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Molecular Dynamics Inc gpu (cuda) version of the amber16 package
Gpu (Cuda) Version Of The Amber16 Package, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/gpu+cuda/amber16+software/pm35653259-345-13-0
Average 90 stars, based on 1 article reviews
gpu (cuda) version of the amber16 package - by Bioz Stars, 2026-11
90/100 stars

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Article Title: The Quasi-Bound State as a Predictor of Relative Binding Free Energy.
Article Snippet: Relative binding free energy (ΔΔGbind) predictions have become the main approach to evaluate the potency of a congeneric series of compounds.. They are enabled by alchemical transformations coupled to free energy methods, tools that have become essential in drug design.. Yet, they are computationally expensive and are limited to small compound sets and relatively simple transformations.


Article Title: Functional characterization and protein engineering of a O-methyltransferase involved in benzylisoquinoline alkaloid biosynthesis of Stephania tetrandra.
Article Snippet: Benzylisoquinoline alkaloids (BIAs) are the primary active components of Stephania tetrandra.. However, the molecular mechanisms underlying BIA biosynthesis in S. tetrandra remain poorly understood.. Here, we reported the isolation and characterization of a novel O-methyltransferase, designated as St7OMT1, from S. tetrandra.

Article Title:
Article Snippet: The docked complex of PPK-1 protein from M. tuberculosis was used for Molecular Dynamics (MD) simulations using the AMBER16 simulation (25-28).

Article Title: Exploring MERTK inhibitor binding mechanisms: insights from adaptive steered molecular dynamics and free energy calculation.
Article Snippet: MERTK, a promising drug target for the treatment of human leukemia and solid tumors, and the development of its small molecule inhibitors holds significant clinical potential.. However, the underlying reasons for the varying activities among these inhibitors and the specifics of their binding mechanism have not been systematically investigated.. By combining conventional molecular dynamics simulations, adaptive steered molecular dynamics simulations and binding free energy calculations based on molecular mechanics Poisson–Boltzmann surface area, the interaction modes of four MERTK inhibitors and dissociation behavior are discussed in detail.

Software:

Article Title: Eutectic Mixtures Based on Oleic Acid and Pulsed Electric Fields: A Strategy for the Extraction of Astaxanthin from Dry Biomass of Xanthophyllomyces dendrorhous .
Article Snippet: .. Molecular dynamics simulations were performed using Assisted Model Building and Energy Refinement software (AMBER18) and General Amber Force Field (GAFF) [26]. ..

Article Title: Scoparone alleviates aortic aneurysm formation by inhibiting smooth muscle cell phenotypic switching and inflammation via mTOR suppression.
Article Snippet: Please cite this article as: Luo, S., Xu, F., Zhong, L., Song, H., Deng, N., Guo, H., Huang, S., You, L., Wei, Y., Li, M., Zuo, S., Zuo, Y., Fan, X., Lei, Y., Liu, Y., Lai, Y., Wang, J., Si, X., Scoparone Alleviates Aortic Aneurysm Formation by Inhibiting Smooth Muscle Cell Phenotypic Switching and Inflammation via mTOR Suppression, Journal of Ethnopharmacology, https://doi.org/10.1016/j.jep.2025.120080.

Molecular Dynamics Simulation:

Article Title: Mechanistic Insights into the Reversible Inhibition of d-Cycloserine in Alanine Racemase from Mycobacterium tuberculosis .
Article Snippet: D-Cycloserine (DCS), an antibiotic used in the treatment of drug-resistant tuberculosis, was traditionally believed to irreversibly inhibit the pyridoxal-5′-phosphate (PLP)-dependent alanine racemase from Mycobacterium tuberculosis (MtAlr).. However, recent research suggests that the inhibition is reversible, as MtAlr can be reactivated by destructing DCS.. This study employs the hybrid quantum mechanics/molecular mechanics (QM/MM) method to investigate the mechanisms of MtAlr inhibition and DCS destruction.

Solvent:

Article Title: Mechanistic Insights into the Reversible Inhibition of d-Cycloserine in Alanine Racemase from Mycobacterium tuberculosis .
Article Snippet: D-Cycloserine (DCS), an antibiotic used in the treatment of drug-resistant tuberculosis, was traditionally believed to irreversibly inhibit the pyridoxal-5′-phosphate (PLP)-dependent alanine racemase from Mycobacterium tuberculosis (MtAlr).. However, recent research suggests that the inhibition is reversible, as MtAlr can be reactivated by destructing DCS.. This study employs the hybrid quantum mechanics/molecular mechanics (QM/MM) method to investigate the mechanisms of MtAlr inhibition and DCS destruction.



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