ABCC Applications Web Page
Welcome to the ABCC Accessible Application Web Page.
From this page, you can get information about our scientific applications and databases. To get more information about any topic, or to run an application, click on any of the mouseover popup menu items on the left-hand side. Program with a tag "Run" is runnable. This site continues to grow, so come back often to check out the many accessible applications available here at the Advanced Biomedical Computing Center (ABCC).
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Other
AutoDock
AutoDock is a suite of programs developed to study how small
molecules such as drug molecules bind to a receptor of known
3D-structure. Please also see the application AutoDockTools (ADT)
which has been specifically developed as a GUI for AutoDock.
Please cite the following reference(s) with the AutoDock results
Morris, G.M., Goodsell. D.S., Halliday, R.S.,
Huey, R., Hart, W.E., Belew, R.K., and Olson, A.J.
(1998) J. Computational Chemistry, 19: 1639-1662.
'Automated Docking Using a Lamarckian Genetic Algorithm
and an Empirical Binding Free Energy Function".
Website: Click Here
insightII
InsightII molecular modeling program is Accelrys' 3D graphical environment for molecular modeling. Its powerful interface gives you a seamless flow of data between other Accelrys' programs. Use
the Insight II program to create, modify, anipulate, display, and analyze molecular systems and related data.
There are many Accelrys programs/modules that can be accessed from InsightII. Please, consult the documentation for more details.
Website: Click Here
MATLAB
MATLAB and companion toolboxes provide an environment for technical computing applications. MATLAB integrates mathematical computing, visualization, and a powerful technical language.
With its more than 600 mathematical, statistical, and engineering functions, MATLAB gives immediate access to high-performance
numerical computing combined with interactive graphical capabilities for creating plots, images, surfaces, and volumetric representations.
MATLAB's Toolboxes extend MATLAB's functionality. ABCC has a license for Statistics Toolbox and Neural Network Toolbox. In addition, the following toolboxes are available at ABCC:
- PRTools, a Matlab toolbox for pattern recognition from Delft University of Technology, The Netherlands is available on SGI systems at /usr/local/fbscapp/prtools3.1.6. The manual is present at /usr/local/fbscapp/prtools3.1.6/PRTOOLS3.pdf. PRTools' website is at
http://www.ph.tn.tudelft.nl/~bob/PRTOOLS.html.
- DIPimage and DIPlib from Delft University of Technology, The Netherlands, is available on SGI systems at /usr/local/fbscapp/dip.
The manual is present at /usr/local/fbscapp/dip/DIPimage.pdf.
DIPimage's website is at http://www.ph.tn.tudelft.nl/DIPlib/.
Website: Click Here
procheck
Checks the stereochemical quality of a protein structure, producing
a number of PostScript plots analysing its overall and
residue-by-residue geometry.
Website: Click Here
CCP4i
CCP4i is the graphical user interface to the ccp4 software suite.
For more information on CCP4I, visit the following web-link
http://www.ccp4.ac.uk/ccp4i_main.html
Website: Click Here
CambridgeDB
The Cambridge Structural Database is the world repository of small molecule crystal structures
The Cambridge Structural Database (CSD) is the principal product the CSD System, which also comprises software for database access, structure visualisation and data analysis, and structural knowledge bases derived from the CSD.
The CSD records bibliographic, chemical and crystallographic information for organic molecules
and metal-organic compounds whose 3D structures have been determined using X-ray diffraction or neutron diffraction.
Website: Click Here
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