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Microsoft .NET Framework 2.0 is required to run the program. |
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Usage |
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The program takes a protein in a FASTA or PDB file as input. |
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Eight sample data (in FASTA and PDB files) are available in the "sample data" folder when you uncompress the file |
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downloaded from this web page. |
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You can also write your sequence in the textbox, and then click "Read Sequence". |
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When you run the program on your own data, set property values by loading sequence entropy, conservation and sequence |
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profile in the following format. "*" in the entropy/conservation column indicates no known value. |
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The format of sequence profile, sequence entropy and conservation. |
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| Sequence profile (sample) |
Entropy(sample) /Conservation(sample) |
| PDB ID: Residue Values |
PDB ID : Residue Values |
1A1R: V 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1A1R: E 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0
1A1R: G 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0
1A1R: E 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0
1A1R: V 98 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1A1R: Q 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0
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1RTL: D *
1RTL: K *
1RTL: N *
1RTL: Q 0.028
1RTL: V 0.192
1RTL: E 0.027
... |
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Click the button "Property Values " to get the values of 6 properties (sequence profiles, ASA values, residue propensity, |
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hydrophobicity, sequence entropy , and conservation) of amino acids. |
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Click the button "Prediction" to find binding sites. It may take a few minutes to find binding sites. Please click OK to start and wait. |
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Prediction results are shown in the Result box. |
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When you load a pdb file, click the "Binding Pairs " button to see binding residue pairs within a distance of 3.5. |
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Tips |
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If you double click the result box, the result is displayed in a new window. |
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Some useful files including the dssp file of your input sequence will be generated in the 'Temp' folder. |
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You may delete the files if you do not need them. |
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