CADD Pipeline

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Contents

About CADD Pipeline

The Computer Aided Drug Discovery (CADD) Pipeline is a workflow environment designed to support molecular dyanmics simulations and virtual screening experiments for in silico drug discovery, with a special focus on supporting the use of the Relaxed Complex Scheme. It includes web based access to applications such as NAMD, AutoDock, PDB2PQR, APBS, MGLToos and couples them in a flexible and scalable fashion through cloud computing. It is developed as a standalone application, using Vision as the backend engine for visual programming and workflow execution. The scientific applications are made accessible through CADD using Opal Web services for scalable and distributed computation.

The workflow components of the CADD pipeline are currently released as Vision networks packaged for specific processes in a modular fashion. These modules may be coupled at ease for more complex processes. In the future, they may also be accessible from workflow repositories such as MyExperiment.org, and from AutoDockTools. The Opal services used in the CADD workflow may be accessed using programmatic access, the Opal Server Dashboard or other workflow clients such as Kepler, VisTrails or Taverna through Opal plugins available at Opal Sourceforge website.

Features

  • Automatic launching of NAMD simulation on TeraGrid and NBCR resources, including experimental support for migration of simulation between resources.
  • Selection of representative snapshots/conformations from MD simulations using clustering tools such as QR factorization from VMD and Ptraj from Amber.
  • Support of Virtual Screening using AutoDock, AutoDock Vina
  • Support of Relaxed Complex Scheme based Virtual Screening and Rescoring
  • Visualization and analysis of Virtual Screening hits

Virtual Screening Libraries

Currently, some libraries are not supported for Autodock virtual screening because they have more ligands than our cluster could support. One could use a filter program to reduce the set of ligands, and then upload to our server for use with your experiment.

Description Support
NCIDS_SC: NCI Diversity Set 1 with rotamers. Prepared 2006 - 2007. Uses ZINC naming scheme. Contains 2282 compounds. yes
NCI_DS3: NCI diversity set 3. yes
sample: a sample database with only 6 ligands. yes
asinex no
chembridge buildingblocks yes
drugbank nutraceutics yes
drugbank smallmol yes
fda approved yes
humanbmetabolome yes
otava no
zinc_natural products no
ZINC library PDBQTs yes


Support

For questions regarding CADD and to report bugs please contact nbcr-admin@ucsd.edu

People

UCSD: Rommie Amaro, Luca Clementi, Wilfred Li, Andy McCammon, Jane Ren (alumni), Nadya Williams.
TSRI: Sargis Dallakyan, Stefano Forli, Ruth Huey, Art Olson, MIchel Sanner, Guillaume Vareille (alumni).

We acknowledge the developers of the following applications accessible through NBCR CADD: NAMD, AutoDock and AutoDock Vina, PDB2PQR, Amber and MGLTools

We acknowledge the following user contributed software services and associated workflows: aMD, Yi Wang, UCSD; AutoClickChem, Jacob Durrant, UCSD.

Downloads

Versions Alpha and Beta are no loner supported.

Installation

Version 0.1.1 (and 0.2) is bundled with MGLTools nightly builds. Please follow MGLtools installation guide available at the download link.

The following procedure is for version 0.1.

Prerequisites

  • MGLTools installed (all platforms).
  • For MacOS X
    X11 is required on Mac OS X, needed by MGLTools.
    Xcode 2.x/3.x is required for installing CADD on Mac OS X.
  • For Windows
    To uncompress and untar downloaded workflows, users will need to use 7zip or WinRAR.

CADD application is distributed with workflows included. The procedure below will work on Linux, MacOS X and Windows platforms.

  1. download CADD_0.1.tar.gz source distribution
  2. unzip and untar using command
    tar xzvf CADD.tar.gz
  3. edit Makefile and set MGL_ROOT and USER variables to your installation:
    For example, on Linux and MacOS:
    MGL_ROOT="/Library/MGLTools/1.5.6" # for MacOS
    USER_HOME = /Users/alice
    on Windows:
    MGL_ROOT = /cygdrive/c/Program\ Files/MGLTools\ 1.5.6
    USER_HOME = /home/alice
    change the following line:
    cp $<MGL_ROOT)/bin/vision cadd.in
    to
    cp $(MGL_ROOT)/vision.bat cadd.in
    comment out the line in the Makefile by adding a # at the beginning:
    # chown -R $(SUDO_USER) $(USER_HOME)/CADDworkflows
    change the following line:
    install -m755 cadd.bin $(MGL_ROOT)/bin/cadd
    to
    install -m755 cadd.bin $(MGL_ROOT)/cadd.bat
  4. run make command:
    make
  5. if no error is given do install:
    sudo su (run this command on linux and MacOS only, it will ask for your laptop password)
    make install

The CADD application files are added to your MGL tool installation and the workflows are saved in $HOME/CADDworkflows/

Notes:

  1. on MacOS it is important to use sudo su command and not su - because Makefile relies on a variable that is set by sudo.
  2. on Windows to use Makefile users will need the default cygwin installation and the Devel..Make package. See the tutorial for cygwin and CADD installation.

Documentation

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