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DBAli. Help/Glossay.
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You can obtain specific information of DBAli in two main ways:
- Quick Help: place your mouse over an image like this one (
 ) to obtain a brief help on the "tool tips".
- Extended Help: click in an image like this one (
 ) to obtain an extended help on the topic your are interested.
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General information
Alignment statistics
Alignment calculations
Updates
Known issues
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General Information
DBAli is a database that includes a coomprehensive all-against-all comparison of protein structures in
the PDB database. All pairwise structural comparisons in DBAli have
been obtained using the MAMMOTH program developed in the group
of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained uwing the SALIGN command
in MODELLER developed in the group of Prof. Andrej Sali.
DBAli uses the Java applet JMol from Dan Gezelter and collaborators
to visualize molecular structures. These are the requirements
in order to properly use the JMol applet. Alternatively, you can also download the
Chimera program to visualize the superimposition PDB files generated by DBAli .
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Alignments statistics
Current statistics of DBAli can be obtained here.
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Alignment Calculations
All pairwise alignment calculations were obtained with the use
of the MAMMOTH program.
All muliple alignment calculations were obtained with the use of the command
SALIGN in the MODELLER program.
Definition of domains and fragments of proteins were obtained ith the program
MODDOM that uses the MCL clustering program.
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Updates
DBAli is automatically updated every week.
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Known issues
- The sorting feature for resulting tables does not properly work with MacOS Safari browser.
- Some PDB entries are not well parsed and will produce an alignment but not a 3D coordinate
files. In those cases, the JMol won't show the superimposition but the alignment will show within
the alignment frame.
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CIPF | SGU Lab | UCSF | Sali Lab | DBAli | MAMMOTH 