Alvaro Cortes Cabrera

Universidad de Alcala de Henares
Laboratorio modelado molecular. Facultad de Medicina.
Centro de Biologia Molecular "Severo Ochoa". CSIC-UAM
Unidad de Bioinformatica

Dr. Ruben Gil-Redondo

Centro de Biologia Molecular "Severo Ochoa". CSIC-UAM
Unidad de Bioinformatica

Dr. Almudena Perona

Centro de Biologia Molecular "Severo Ochoa". CSIC-UAM
Unidad de Bioinformatica

Dr. Federico Gago

Universidad de Alcala de Henares
Laboratorio modelado molecular. Facultad de Medicina.

Dr. Antonio Morreale

Centro de Biologia Molecular "Severo Ochoa". CSIC-UAM
Unidad de Bioinformatica

Table of Contents
License
License agreement
Disclaimer
Introduction
Introduction
Installation
From Source
Server side requirements
Client side requirements
Overview
Obtaining VSDMIP
MySQL Database Management System installation and setup
Installing queue system
Installing VSDMIP platform included software
Configuring remote access without password prompt
From Binary distribution
Supported systems
Common steps
Scientific Linux and Red Hat Enterprise server clones
Debian and clones (Ubuntu)
Database modules and schema
Windows installation
Plugin installation
Database reference
Overview
Tables
ORIGINDB
MOLECULE
CONFIGURATION
CONFORMER
DOCK_FILTER
RESULT_DF
VIRTUAL_SCREENING
RESULT_VS
FINGER_TYPE
FINGERPRINTS
PHARMACOPHORES
ATOM_CODE
ALFA_TYPE
User defined functions
MolSearch_tanimoto
MolSearch_tversky
MolSearch_rule
selectfp
kl_analisis
MolSearch_fusion
centroids
VSDMIP command reference
getMol2.exe
getPDBforCDOCK3.exe
getResultsFromDOCK.exe
getResultsFromVS.exe
insertVSDB.exe
runAutoDock.exe
runCDOCK3.exe
runDelPhiAndApolar.exe
runDOCKFilter.exe
runFredFilter.exe
runISM.exe
runRocsFilter.exe
runGTP.exe
Configuration files.
<dbconfig>
<logFile>
<queue>
<queue-folder>
<programs>
<querys>
CGRID.exe
CDOCK.exe
ALFA.exe
GTP.exe
GF.exe
VSDMIP Pymol Plugin
Application description
Working examples
Introduction
Example 1: Simple docking
Example 2: Simple Stucture-based Virtual Screening
Example 3: Simple Ligand-based Virtual Screening
Example 4: Advanced Ligand-based Virtual Screening
Example 5: Mixing Ligand and Structure VS approaches
Glossary