adaptive runge-kutta solver ode45  (MathWorks Inc)

Journal: Frontiers in Bioinformatics

Article Title: Identification of novel drug targets for Helicobacter pylori : structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway

doi: 10.3389/fbinf.2024.1482338

Figure Lengend Snippet: The interactions of 6,8-Dihydroxyisocoumarin-3-carboxylic acid (A) and Epicatechin (B) with DAH7PS protein. The tertiary structure of the DAH7PS protein and its APBS (Adaptive Poisson-Boltzmann Solver) electrostatic interactions with the ligands are shown in (D) and (C) depictions. Data highlight that the pocket size has a highly positive charge.

Article Snippet: ADMET, Absorption, Distribution, Metabolism, Excretion, and Toxicity; APBS, Adaptive Poisson-Boltzmann Solver; CADD, Computer Aided Drug Discovery; DEGs, Database of essential genes; DAH7PS, 3-deoxy-D-arabino-heptulosonate 7-phosphate; E4P, Erythrose 4-phosphate; FDA, Food and Drug Administration; KEGG, Kyoto Encyclopedia of Genes and Genomes; KAAS, KEGG Automatic Annotation Server; MALT, Mucoid Associated Lymphoid Tissue; MD, Molecular Dynamics; MSA, Multiple Sequence Alignment; NCBI, National Centers for Biotechnology Information; NMR, Nuclear Magnetic Resonance; NPT, Constant Number of particles, Pressure, and Temperature; NVT, Constant Number of particles, Volume, and Temperature; PME, Particle Mesh Ewald; PEP, Phosphoenolpyruvate; PDB, Protein Data Bank; PPI, Proton Pump Inhibitor; Rg, Radius of Gyration; RMSD, Root Mean Square Deviation; RMSF, Root Mean Square Fluctuation; RO5, Lipinski’s Rule of Five; SBVS, Structure Based Virtual Screening; SPC, Simple Point Charge; VDW, Van Der Waals; WHO, World Health Organization.

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