BT 652: Scoring Small Molecule Leads and Docking Analysis

This set of vocabulary flashcards covers the computational docking terminology, software, and parameters outlined in the BT 652 Biotechnology lab schedule and instructions.

BT 652

The course code for the Biotechnology Program schedule for Summer $2026$ at the University of Alabama at Birmingham.

ABC Transporters

The protein category assigned for bioinformatical analysis, sequence alignments, structural analysis, and docking runs.

Pymol

The software used for structural analysis, making figures, displaying transporter sequences, and hosting the DockingPie plugin.

DockingPie 1.2

A Pymol plugin used to import receptors, set grid parameters, and computationally test selected ligands through docking analysis.

Vina

A specific tab within the DockingPie window used to navigate receptors and initiate docking runs.

SDF files

The 3D small molecule file format used for the library files loaded into Pymol for computational docking.

PDB file

The protein structure file format loaded into Pymol to represent the ABC transporter.

PubChem

The platform navigated for the retrieval of small molecules during Week 3 and Week 4 of the lab.

kcal/mol

The unit of measurement, specifically $kcal\,mol^{-1}$, used for scoring small molecule leads by theoretical $K_d$ values.

Exhaustiveness

A parameter in the Docking tab that must be set to a value above $5$.

Poses

A setting in the Docking tab that determines the number of results, required to be set to a minimum of $20$ or more.

Grid dimensions

Parameters adjusted in the grid settings tab where 'All' is set to $4$ and individual $x, y, z$ values are modified as needed.

Grid Coordinates

The $x$, $y$, and $z$ settings adjusted to ensure the grid box covers the proposed ligand binding area.

AutoDock4

A computational docking tool introduced during Week 5 alongside AutoDock Vina.

Receptor Generation Parameters

Specific settings applied to the ABC transporter including: Add Hydrogens, Remove all nonstandard residues, remove water, and Show Heteroatoms.