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Revision 1.3 - (download) (as text) (annotate)
Sat Feb 4 03:10:09 2006 UTC (14 years, 4 months ago) by hwang
Branch: MAIN
CVS Tags: HEAD
Changes since 1.2: +49 -29 lines
ShowTable.pl:
-took out underscore, improve download feature, improve layouts, sort by author enabled, link to subsystem
ShowTableKey.pl
-improve column description
drug_targets.pl
-link to current list


use CGI;

my $cgi = new CGI;
print $cgi->header();
print $cgi->head($cgi->title("Column Keys"));
print $cgi->start_body();
print 

"    
    <h2>Genus, Author</h2><p>
    This column names genus of the organims and the primary author.
    <p>

    <h2>Category</h2><p>
    
    Category lists one of the following DrugTarget Category Codes:<p>  ES == Essential<p> ES-X == Essential determined by experiment<p> ES-L == Essential from the literature<p>  KA-T == Known Antibiotic target<p> KA-I == Known Antibiotic Inhibitor<p> VA == Virulence associated<p> VA-K == known virulence associated<p> VA-P == putative virulence associated
<p>
    <h2>Identifier, by Author</h2><p>
    
     This column contains the specific identifier from the literature and the associated author. The link is to the PubMed listing of the publication where the identifier was referenced.
    <p>
    <h2>Aliases from SEED</h2><p>
    All Aliases were taken from from NMPDR protein page.
    <p>
    <h2>Peg Id</h2><p>
    The PEG ID is a internal identifyer for the specific NMPDR protein page.
    <p>  
    <h2>Protein Sequence length</h2><p>
    The Protein Sequence length, the number of amino acids.
    <p>
    <h2>GenBank Id</h2><p>
    The GenBank id is the gene identification number in GenBank. The link will take you to the entry in GenBank.
    <p>
    <h2>UniProt Id</h2><p>
    The UniProt ID is the gene identification number in UniProt. The link will take you to the entry in UniProt.
    <p>
    <h2>Functional Role</h2><p>
    The Functional Role is the SEED Annotation for the PEG ID
    <p>
    <h2>Conservation of Seqs</h2><p>
    For a given gene, Conservation of Seqs searches for homologs in a defined group of phylogeneticly distant organisms (10 for Gram-Positive and 10 for Gram-Negative), aligns the resulting 10 sequences and then computes the degree of conservation from the aligned sequence matrix. A perfectly conserved sequence family has the value 1. When computing the degree of conservation at a certain site 'i' of the aligned sequences, the following formula is used:<p> 
    con(i) = Sum { (number of appearances of a non-gap character)^2 } / (number of non-gap characters)^2.<p> 
    The overall degree of conservation is the weighted sum of con(i)s at all sites, with weight w(i) proportional to the number of non-gap characters at site i.
    <p>
    <h2>PDB (bound)</h2><p>
    The Protein Data Base is an archive of experimentally-determined, biological macromolecule 3-D structures from the Brookhaven National Laboratory.   We have found Capturing ligand binding information is useful for docking studies.  As a result we created a convention to separate PDB entries into PDB bound and PDB free.  A PDB is bound when the pdb file description contains the words 'COMPLEX' or 'COMPLEXED', and/or if the HETATM (hetrogeneous atom) are not small molecules.  PDB bound searches PEG Protein Sequence against the PDB bound Protein Sequences to find the best hit. 
    <p>
    <h2>PDB (bound) EVAL</h2><p>
    Compares the PEG Sequence and the PDB Sequence and returns the e Value, the lower the e Value  the better the match (with 0.0 being perfect match). 
    <p>
    <h2>PDB (free)</h2><p>
    PDB free searches PEG Protein Sequence against the PDB free Protein Sequences to find the best hit. see above
    <p>
    <h2>PDB (free) EVAL</h2><p>
    Compares the PEG Sequence and the PDB Sequence and returns the e Value, the lower the e Value  the better the match (with 0.0 being perfect match). 
    <p>
    <h2>PDB (free) Title</h2><p>
    Title of the PDB (free) file as reported by PDB: http://www.rcsb.org/pdb/
    <p>
    <h2>PDB SeqLen</h2><p>
    The amino acid length of the protein in the PDB (free) file as reported by PDB.
    <p>
    <h2>ProtDist</h2><p>
    ProtDist compares specific amino acid sequence to the PDB (free) Protein Sequence.  Where the amion acids are dissimilar ProtDist computes a distance model of amino acid replacement. Lower ProtDist scores correlate to more similar sequences. http://evolution.genetics.washington.edu/phylip.html,
    <p>
    <h2>PASS ASPs</h2><p>
     PASS [Putative Active Sites with Spheres] takes PDB (free) file and uses geometry to identify positions likely to represent binding sites based upon the size, shape, and burial extent of these volumes. PASS generates ASP [Active Site Points] files in gif format.  The column entry will bring up the PASS ASP gif file.  The number in the colunm represents the number of ASP that PASS found.  http://www.ccl.net/cca/software/UNIX/pass/overview.shtml,
     <p>
     <h2>PASS Weight of Largetst Pocket</h2><p>
     PASS generates Pockets Predictions putatively where ligand-protein interaction would occur.  PASS Weight of Largest Pocket is a score given by PASS to the largest pocket identified.  http://www.ccl.net/cca/software/UNIX/pass/overview.shtml
     <p>
     <h2>PDB Ligand and CLiBE</h2><p>
    CLiBE A Database of Computed Ligand Binding Energy for Ligand-Receptor Complexes and Its Potential Use in the Analysis of Drug Binding Competitiveness. X. Chen, Z. L. Ji, D.G. Zhi, and Y. Z. Chen, Comp. Chem. 26, 661-666(2002).<p>
    If a PDB (bound) exists then the Ligand of the bound PDB is searched against CLiBE (Computed Ligand Binding Engergy)  database.  The column entry links you to CLiBE page on the specific ligand. http://xin.cz3.nus.edu.sg/group/clibe/clibe.asp
    <p>
    <h2>Total Energy</h2><p>
     Ligand-Receptor Interaction Energy (in Kcal/mol) as reported by CLiBE. http://xin.cz3.nus.edu.sg/group/clibe/clibe.asp
    <p>
    <h2>Van der Waals Interactions</h2><p>
      Ligand-Receptor Interaction Energy (in Kcal/mol) as reported by CLiBE. http://xin.cz3.nus.edu.sg/group/clibe/clibe.asp
    <p>
    <h2>Hydrogen Bond</h2><p>
     Ligand-Receptor Interaction Energy (in Kcal/mol) as reported by CLiBE. http://xin.cz3.nus.edu.sg/group/clibe/clibe.asp
    <p>
    <h2>Electrostatic Interaction</h2><p>
     Ligand-Receptor Interaction Energy (in Kcal/mol) as reported by CLiBE. http://xin.cz3.nus.edu.sg/group/clibe/clibe.asp
    <p>
    <h2>Solvation Energy</h2><p>
     Ligand-Receptor Interaction Energy (in Kcal/mol) as reported by CLiBE. http://xin.cz3.nus.edu.sg/group/clibe/clibe.asp

";

print $cgi->end_body();

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