Index of /~nanjiang/zincpred/suppliment

      Name                    Last modified       Size  Description


[DIR] Parent Directory        20-Jan-2011 11:01      -  
[TXT] background_amino_aci..> 03-Dec-2007 14:31     1k  
[TXT] closeZnManuallyCurat..> 19-Sep-2007 19:25     4k  
[TXT] closeZnPro1-5.txt       19-Sep-2007 19:26    55k  
[TXT] closeZnPro3-5.txt       19-Sep-2007 19:26    48k  
[   ] encoding-single-site..> 03-Dec-2007 16:43    26k  
[TXT] matrices-for-encodin..> 03-Dec-2007 14:33     1k  
[TXT] passe.idlist.txt        22-Nov-2006 14:01    16k  
[   ] profiles-used-in-Seg..> 09-Dec-2007 16:38    33k  
[   ] supplementary-figure..> 09-Oct-2007 17:05   281k  

1 closeZnPro1-5.txt
  A list of all 235 protein chains (and their residues) that bind to zinc.

2 closeZnPro3-5.txt
  A list of all 210 protein chains (and their residues) that bind to Zn3, Zn4
  or Zn5. Zn3, Zn4 and Zn5 are Zn atoms that bind to 3, 4 and 5 amino acid residues
  respectively.

3 closeZnManuallyCurated.txt
  A list of 8 manually curated zinc-binding proteins (and their residues).

4 passe.idlist.txt
  Chain identifiers for 2,727 unique protein chains.

5 background_amino_acid_frequency.txt
  Background amino acid composition for 20 amino acids.

6 matrices-for-encoding.txt
  Matrices for encoding different parameters for generating SVM features
  vectors.

7 encoding-single-site-vector-pair-based-vector.doc
  Description for encoding single-site vectors and pair-based vectors

8 supplementary-figures.doc
  Supplementary figures:
  Figure 1: Illustration about how to encode a single-site vector and a pair-based vector
  Figure 2: Fraction of conserved zinc-binding residues out of all zinc-binding residues and (b) Fraction of conserved residues out of all residues cutting at different conservation score levels for Cys, His, Asp and Glu separately. 
  Figure 3: Zinc-binding sites of liver alcohol dehydrogenase-NADH complex (PDB code 2OHX)
  Figure 4: An example of a protein that possibly does bind zinc in vivo, although no zinc was present in the crystals. 

9 profiles-used-in-Segment-Matching-Method.doc
  A brief description about how the profiles used in the Segment Matching Method are built.
  
  
References:

  Nanjiang Shu, Tuping Zhou and Sven Hovmöller, "Prediction of Zinc-Binding
  Sites in Proteins From Sequence"