Computational protocol: Sequence Specific Binding of Beta Carboline Alkaloid Harmalol with Deoxyribonucleotides: Binding Heterogeneity, Conformational, Thermodynamic and Cytotoxic Aspects

Similar protocols

Protocol publication

[…] Rigid body molecular docking calculations were accomplished using AutoDock-vina program (version 1.1.2) from the Scripps Research Institute . Autodock-vina performs faster and more accurate docking calculations than autodock –. Autodock-Vina has been used earlier for ligand-DNA docking studies . In rigid-body docking method, the DNA structure remains rigid while the ligand remains flexible. This enables the ligand to explore possible binding poses within a specified area on the receptor. To utilize the intercalation cavity in both the PDB files, the original ligands contained in the PDB files were removed manually using MOE (molecular operating environment) program. The resulting DNA structures were then energy minimized in MOE program by using AMBER99 force field with a tether weight of 10 on heavy atoms to obtain modified DNA duplexes having an empty intercalation cavity. Before docking, the receptor and ligand coordinate files were converted into PDBQT format using MGLTools (version 1.5.4). For docking calculations with the modified 4BZV, a 3-dimensional grid box of 28 × 30 × 28 was prepared with a grid spacing of 0.375 Å. The grid was centered on coordinates x = 28.929, y = 33.513, z = 34.682. In the case of the modified 1G3X, the grid box dimension was 38 × 24 × 48 and the grid box center was at x = 57.642, y = 52.855, z = 58.635 with a grid spacing of 0.375 Å. For each docking calculation, 20 different poses were requested within the energy range of 2 kcal/mol. Due to the large search space volume, the exhaustiveness of the calculation was increased to 16 which is the 2 times the default value in autodock-vina. All other parameters were kept at their default values. The analysis and representation of docked poses were performed using Discovery Studio Visualizer from Accelrys Inc. and UCSF Chimera programs. […]

Pipeline specifications

Software tools AutoDock Vina, Discovery Studio® Visualizer, UCSF Chimera
Application Protein interaction analysis
Diseases Drug-Related Side Effects and Adverse Reactions
Chemicals Deoxyribonucleotides, Poly dA-dT, Polynucleotides