Difference between revisions of "2023 DOCK tutorial 2 with PDBID 3WZE"
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= Introduction = | = Introduction = | ||
| − | == | + | Oftentimes, a protein whose function is found to be involved in one or more diseases may become a target of interest for pharmaceutical design. The most common methodology for designing such inhibitors is to design a molecule which can compete with the enzyme's native substrate for the enzyme's active site. Thus, many pharmaceuticals are competitive inhibitors of their protein targets, and can be best designed by finding molecules that bind well to the target's active site. If the target protein's structure is known, and the active pocket can be identified, then performing a virtual screen can be a monetarily and temporally efficient method of identifying candidate molecules for further testing as potential pharmaceuticals. |
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| + | A virtual screen is set up by downloading a large library of drug-like molecules from a database such as ZINC '''[REFERENCE]''' | ||
| + | |||
| + | == Software == | ||
| + | |||
| + | === DOCK6.10 === | ||
| + | |||
| + | === Chimera === | ||
| + | |||
| + | === ChimeraX (optional) === | ||
| + | |||
| + | === Alphafoldd2 (optional) === | ||
== Using the Terminal == | == Using the Terminal == | ||
| + | |||
| + | = References = | ||
Revision as of 17:02, 4 March 2023
In this tutorial, you will learn how use the program DOCK6.10 to perform a virtual screen, in which you assess how well the molecules in a library of drug-like molecules bind to a protein of known structure.
Contents
Introduction
Oftentimes, a protein whose function is found to be involved in one or more diseases may become a target of interest for pharmaceutical design. The most common methodology for designing such inhibitors is to design a molecule which can compete with the enzyme's native substrate for the enzyme's active site. Thus, many pharmaceuticals are competitive inhibitors of their protein targets, and can be best designed by finding molecules that bind well to the target's active site. If the target protein's structure is known, and the active pocket can be identified, then performing a virtual screen can be a monetarily and temporally efficient method of identifying candidate molecules for further testing as potential pharmaceuticals.
A virtual screen is set up by downloading a large library of drug-like molecules from a database such as ZINC [REFERENCE]
