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hemeBIND
hemeNet
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HemeNet Manual

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Methodology

HemeNet is a novel algorithm for heme-binding residue prediction by representing protein

structures as residue interaction networks. Four well known network-based features, such

as degree, closeness, betweenness and clustering coefficient are extracted from the network

for each residue. In combination with conventional features, including PSSM, ASA, DPX and

CX, these topological features can significantly improve the predicton performance of

heme-binding residues by using support vector machine.

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Input Format

The input of HemeNet is a PDB file as following:

ATOM 1 N MET A 1 19.555 29.903 42.490 1.00 50.76 N

ATOM 2 CA MET A 1 20.614 30.851 42.171 1.00 54.92 C

ATOM 3 C MET A 1 21.995 30.221 42.321 1.00 56.63 C

ATOM 4 O MET A 1 22.237 29.387 43.195 1.00 55.52 O

ATOM 5 CB MET A 1 20.491 32.089 43.048 1.00 60.12 C

ATOM 6 N LEU A 2 22.910 30.635 41.449 1.00 47.67 N

ATOM 7 CA LEU A 2 24.304 30.230 41.561 1.00 39.94 C

ATOM 8 C LEU A 2 25.108 31.273 42.334 1.00 37.57 C

ATOM 9 O LEU A 2 25.342 32.368 41.821 1.00 58.96 O

ATOM 10 CB LEU A 2 24.921 30.038 40.176 1.00 40.96 C

ATOM 11 CG LEU A 2 24.451 28.823 39.376 1.00 40.06 C

ATOM 12 CD1 LEU A 2 24.794 28.991 37.903 1.00 38.65 C

ATOM 13 CD2 LEU A 2 25.054 27.548 39.941 1.00 31.43 C

ATOM 14 N SER A 3 25.535 30.937 43.543 1.00 31.50 N

ATOM 15 CA SER A 3 26.465 31.776 44.291 1.00 30.86 C

ATOM 16 C SER A 3 27.633 32.236 43.430 1.00 37.53 C

ATOM 17 O SER A 3 27.927 31.657 42.381 1.00 34.29 O

ATOM 18 CB SER A 3 27.032 30.985 45.481 1.00 33.36 C

ATOM 19 OG SER A 3 28.180 30.254 45.070 1.00 29.16 O

* Note that the file should only contain the lines that begin with 'ATOM' and

provide at least 15 residues having atomic coordinates.

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Output Format

Pos AA Score Tag

1 A 0.15 -

2 C 0.76 +

3 T 0.27 -

4 K 0.18 -

5 N 0.14 -

6 A 0.19 -

7 I n/a B

8 A 0.08 -

9 Q 0.23 -

10 T 0.06 -

11 G 0.10 -

12 F 0.74 +

13 N 0.09 -

14 K 0.05 -

15 D n/a B

16 K 0.09 -

17 Y 0.77 +

18 F 0.62 -

19 N 0.06 -

20 G 0.21 -

* +: binding residue -: non-binding residue B: buried residue

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Citation

Rong Liu, Jianjun Hu. (2011) Computational prediction of heme-binding residues

by exploiting residue interaction network. Submitted.

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Contact

Dr. Rong Liu

Dr. Jianjun Hu

Department of Computer Science and Engineering

University of South Carolina

Columbia, SC 29208

E-mail: liurong116@tom.com or jianjunh@cse.sc.edu