AutoDock Atom Types

AutoDock is an educational platform that uses known atoms and a grid interface in combination with bonding applications to predict the binding rate of most small molecules. This allows students to virtually study molecule binding without requiring expensive laboratory time and training.

Elements

• AutoDock supports the basic elements: H, C, N, O, F, Mg, P, S, Cl, Ca, Mn, Fe, Zn, Br and I. These have been parametrized within the program so that it recognizes their physical characteristics, attributes and reactions to other elements. These basic elements may be used to form a molecule and tested with a binding application or solvent. For Example, a student would indicate two hydrogen molecules to one oxygen molecule, H2O and would be able to test this water molecule against its binding rate.

Binding

• AutoDock supports a variety of binding or docking chemicals and elements, the name and or label of the docking element should be typed into the user interface to locate and select the proper element. AutoDock provides a system of tools designed to help view, monitor and expedite the bonding process. These include X-ray crystallography; structure-based drug design, lead optimization, virtual screening (HTS), combinatorial library design, protein-protein docking and chemical mechanism studies. This allows a student to work with the elements and to bond them under a variety of conditions so that the best and most accurate test results can be achieved.

Grid Map

• AutoDock's grid or Grid Map is used to pair and match elements with binders; to do so, the student should enter the chemical name of the element in single letter format to locate it on the grid. Elements on the grid have already been studied and tested and their perimeters have already been defined. This allows a student to simply select an atom and binder without having to enter details. The AutoDock Grid Map therefore allows a student to learn about the properties and perimeters of the atom while testing its binding rate.

Adding Elements

• Should a student have an element that has not yet been entered into AutoDock's system, they may enter it using AutoDock's pre-existing perimeter file with the exact detailed information about the atom in question. This should then be uploaded to AutoDock and calibrated, re-calibrated for accuracy before being tested. However, it should be noted that adding an element requires an in-depth knowledge of how the element will act and react during the bonding process as well as with other atoms.