Computational protocol: Biochemical Mechanisms for Geographical Adaptations to Novel Toxin Exposures in Butterflyfish

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Protocol publication

[…] Ligands and crystal structures were prepared for docking using AutoDockTools v1.5.4; [], with the addition of polar hydrogens and the assignment of Gasteiger charges. Ligand structure and charge minimization was performed with semi-empirical methods (PM6 Hamiltonian in Mopac2009) []. Gasteiger-Marsili partial charges were used in the final docking runs. High throughput docking was performed using Autodock Vina (v1.1.2)[]. Flexible ligands were docked into models with rigid protein backbones and rigid side chains. 100 replicate dockings were performed, retaining a broad range of calculated energies (6 kcal/mol). Docking visualization was performed using PyMol (v., Schrödinger LLC, Portland, OR). […]

Pipeline specifications

Software tools AutoDock, AutoDock Vina, PyMOL
Application Protein interaction analysis
Organisms Spirogyra maxima
Chemicals NADP