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amber20 software package 31 (Molecular Dynamics Inc)

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Molecular Dynamics Inc amber20 software package 31
Amber20 Software Package 31, 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/software+packages/amber20/pm42300623-184-7-0
Average 86 stars, based on 1 article reviews

amber20 software package 31 - by Bioz Stars, 2026-09

86/100 stars

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Article Title: Myristoylation licenses disordered viral VP4 protein to anchor to and perforate the membrane through phase separation
Article Snippet: Molecular dynamics simulations were performed using the Amber20 and GROMACS 2020/22 package, with detailed protocol reported in the method section of the manuscript.

Article Title: Structural Characterization of Glycolytic Enzymes from Trypanosoma cruzi.
Article Snippet: Trypanosoma cruzi, the etiological agent of Chagas disease, depends on glycolysis for ATP production, rendering its glycolytic enzymes attractive targets for therapeutic development.. Here, we report the highresolution crystal structures of two essential glycolytic enzymes, glucose-6-phosphate isomerase (Tc PGI, 1.8 Å) and enolase (Tc enolase, 2.4 Å) and provide structural and computational analyses to support structure-based drug design.. Tc PGI adopts a dimeric αβα sandwich fold and features a parasite-specific 53residue N-terminal extension and a unique C-terminal hook region which both distinguish it from its human ortholog.

Article Title: Molecular Dynamics Simulations Provide Further Insights into the Allosteric Regulation of the Kinesin-5 Motor Domain by Loop 5.
Article Snippet: Molecular dynamics simulations were performed using Amber20.77 The 4 systems (ADP, ADPfil, apo, ATP) were first minimized by Steepest Descent and Conjugate Gradient methods, initially for 300 steps with positional restraints on all atoms except hydrogen and water and then another 300 steps without restrictions.

Article Title: Enhancing prebiotic production by engineering the levanbiose-binding site of Erwinia tasmaniensis levansucrase
Article Snippet: Molecular dynamics (MD) simulations were performed with Amber20 (ref. ) following protocols adapted from previous studies.

Generated:

Article Title: Functional and structural characterization of the SARS-CoV-2 spike N481K mutation.
Article Snippet: .. Molecular dynamics of wild-type and N481K complexes To assess the structural conformations of the generated complexes within a dynamic environment, we employed the amber20 package along with the FF19SB force field [20, 21] to conduct molecular dynamics simulations of wildtype and N481K complexes. ..

Derivative Assay:

Article Title: Design, synthesis, and anti-colorectal cancer activity of quinoxalines with improved drug-like properties.
Article Snippet: Colorectal cancer (CRC) is strongly associated with aberrant activation of the PI3K/Akt/mTOR pathway, in which PI3Kα represents a clinically validated therapeutic target.. Herein, we report the rational design, synthesis, and biological evaluation of quinoxaline derivatives as potent PI3Kα selective inhibitors derived from the lead compound 18a, which was developed in our previous study and suffered from poor drug-like properties.. Structure-guided modification led to the identification of compound 8b, which exhibited remarkably improved solubility and oral bioavailability, and it showed nano-mol level inhibitory activity against PI3Kα.

Software:

Article Title: Thermodynamics, structure, and antibacterial activity of the decavanadate-lysozyme complex.
Article Snippet: This study investigated the influence of highly charged polyanions on protein structure and function using the lysozyme-decavanadate ([V10O28] ) system as a model. To elucidate the thermodynamic, structural, and functional consequences of these interactions, the binding was comprehensively characterized using an integrated experimental and computational approach, including isothermal titration calorimetry (ITC), steady-state fluorescence spectroscopy (SF), electrospray ionization mass spectrometry (ESI-MS), circular dichroism spectroscopy (CD), and molecular dynamics (MD) simulations.. The formation of a 2:1 ([V10O28] :lysozyme) complex at pH 5.0 was established using ITC and SF data, with MD simulations localizing the primary binding site to the positively charged C-terminal region of the protein.. The complex is predominantly stabilized by electrostatic interactions, consistent with the observed enthalpy-driven binding thermodynamics.