Difference between revisions of "2020 DOCK tutorial 1 with PDBID 3VJK"
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| − | + | = Introduction = | |
| + | |||
| + | Welcome to the Rizzo lab! | ||
| + | |||
| + | This tutorial is provided by the students of stony brook to help the community better understand the DOCK toolset. | ||
| + | |||
| + | == Software packages == | ||
| + | To follow this tutorial you will need to have the following programs installed: | ||
| + | |||
| + | DOCK | ||
| + | sing-something | ||
| + | |||
| + | At several points this tutorial will reference these programs as commands in a shell environment. The students who did this ran their programs on a UNIX (CoreOS or Ubuntu) server, although this process should generalize to your specific setup. For help, please reference available documentation. | ||
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| + | = Background = | ||
| + | = Object preparation = | ||
| + | = Protein = | ||
| − | = | + | = Ligand = |
| − | + | = Sphere Selection = | |
| + | Generate an INSPH file | ||
[your_receptor].dms | [your_receptor].dms | ||
| Line 22: | Line 37: | ||
1.4 //Size of sphere that rolls over dms file surface for cavities | 1.4 //Size of sphere that rolls over dms file surface for cavities | ||
[your_receptor].sph | [your_receptor].sph | ||
| + | |||
| + | = Box localization = | ||
| + | |||
| + | |||
| + | = Grid formation = | ||
Revision as of 15:20, 14 February 2020
Contents
Introduction
Welcome to the Rizzo lab!
This tutorial is provided by the students of stony brook to help the community better understand the DOCK toolset.
Software packages
To follow this tutorial you will need to have the following programs installed:
DOCK sing-something
At several points this tutorial will reference these programs as commands in a shell environment. The students who did this ran their programs on a UNIX (CoreOS or Ubuntu) server, although this process should generalize to your specific setup. For help, please reference available documentation.
Background
Object preparation
Protein
Ligand
Sphere Selection
Generate an INSPH file
[your_receptor].dms R //Spheres will be generated outside the protein surface X //All points are used 0.0 //Distance that steric interactions are checked 4.0 //Maximum sphere radius of generated sphere 1.4 //Size of sphere that rolls over dms file surface for cavities [your_receptor].sph
