Ligands were prepared for docking using the Sybyl 7.3 Molecular Modeling Suite of Tripos, Inc. 3D conformations were generated using Concord 4.051 , hydrogen atoms were added and charges were loaded using the Gasteiger and Marsili charge calculation method.52 Basic amines were protonated and acidic carboxyl groups were de-protonated prior to charge calculation. The AMPPD ligand was minimized with the Tripos Force Field prior to docking using the Powell method with an initial Simplex53 optimization and 1000 iterations or gradient termination at 0.01 kcal/(mol*A). Input ligand file format was mol2 for all docking programs investigated.
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Ligand Preparation for Molecular Docking
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Other organizations : University of Tennessee Health Science Center, St. Jude Children's Research Hospital
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Variable analysis
independent variables
- Preparation of ligands using Sybyl 7.3 Molecular Modeling Suite of Tripos, Inc.
- Generation of 3D conformations using Concord 4.051
- Addition of hydrogen atoms and charge calculation using the Gasteiger and Marsili method
- Protonation of basic amines and deprotonation of acidic carboxyl groups prior to charge calculation
- Minimization of the AMPPD ligand with the Tripos Force Field prior to docking
- Docking of the prepared ligands
- Input ligand file format being mol2 for all docking programs investigated
- Powell method with an initial Simplex optimization and 1000 iterations or gradient termination at 0.01 kcal/(mol*A) used for minimization
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