Computational protocol: Binding Modes of Three Inhibitors 8CA, F8A and I4A to A-FABP Studied Based on Molecular Dynamics Simulation

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Protocol publication

[…] The initial coordinates of 8CA, F8A and I4A/A-FABP complexes were obtained from the protein data bank and their PDB entry are 3FR2, 3FR4 and 3FR5, respectively . All crystal water molecules were retained in the starting model. FF03 force field was used to produce the parameters of protein and water molecules . The general amber force field was assigned to the three inhibitors . The am1-bcc method implemented in Amber12 was applied to assign the partial atomic charges to the three inhibitors , . The side-chain protonation states were assigned at PH = 7.0 by using PROPKA program , . Each system was solvated in a truncated octahedron box of TIP3P water molecules with a 12.0 Å buffer along each dimension . An appropriate number of sodion counterions were added to produce a neutral charge on the system. […]

Pipeline specifications

Software tools AMBER, PROPKA
Application Protein structure analysis
Diseases Metabolic Diseases, Genetic Diseases, Inborn, Atherosclerosis