Difference between revisions of "2021 DOCK tutorial 3 with PDBID 1S19"
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===DOCK=== | ===DOCK=== | ||
| − | [ | + | Developed by Irwin D. Kuntz, Jr. and colleagues at UCSF, DOCK is a program used to dock molecules to one another. Docking is a process in which given a small molecule or ligand in the active site of a receptor, the program will try to predict the lowest-energy binding mode of the ligand to the receptor. This process is very important in drug discovery as small molecules that bind to or interact with the active site of a receptor associated with a disease could inhibit its function, acting as a drug. DOCK is a particularly helpful tool as it is used to screen massive libraries of molecules, containing millions of compounds, against a receptor to identify the most promising drug lead compounds. |
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| + | DOCK historically used a geometric matching algorithm to superimpose the ligand onto a negative image of the active site of the receptor. Over the years, features were added that would improve the programs ability to find the lowest-energy binding mode. Somem of these features include force-field based scoring, on-the-fly optimization and an algorithm for flexible ligand docking. | ||
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| + | In this tutorial DOCK6 will be used. New features for DOCK6 include: additional scoring options during minimization; DOCK 3.5 scoring-including Delphi electrostatics, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screening and more (see UCSF DOCK[http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm]). These new features improved the programs ability to predict binding poses. | ||
===1S19=== | ===1S19=== | ||
Revision as of 09:55, 23 February 2021
Contents
Introduction
DOCK
Developed by Irwin D. Kuntz, Jr. and colleagues at UCSF, DOCK is a program used to dock molecules to one another. Docking is a process in which given a small molecule or ligand in the active site of a receptor, the program will try to predict the lowest-energy binding mode of the ligand to the receptor. This process is very important in drug discovery as small molecules that bind to or interact with the active site of a receptor associated with a disease could inhibit its function, acting as a drug. DOCK is a particularly helpful tool as it is used to screen massive libraries of molecules, containing millions of compounds, against a receptor to identify the most promising drug lead compounds.
DOCK historically used a geometric matching algorithm to superimpose the ligand onto a negative image of the active site of the receptor. Over the years, features were added that would improve the programs ability to find the lowest-energy binding mode. Somem of these features include force-field based scoring, on-the-fly optimization and an algorithm for flexible ligand docking.
In this tutorial DOCK6 will be used. New features for DOCK6 include: additional scoring options during minimization; DOCK 3.5 scoring-including Delphi electrostatics, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screening and more (see UCSF DOCK[1]). These new features improved the programs ability to predict binding poses.
1S19
[Paragraph about 1S19]
Chimera
[Paragraph about Chimera]
Making Directories
[Brief thing on creating the different folders]
Preparing the Ligand and Receptor
PDB Structure
Download the structure of 1S19 from the Protein Data Bank (PDB) File:Example.jpg
