PMID- 15047913
OWN - NLM
STAT- in-process
DA  - 20040329
IS  - 1741-0126
VI  - 17
IP  - 2
DP  - 2004 Feb
TI  - Prediction of protein-protein interaction sites using support vector
      machines.
PG  - 165-73
AB  - The identification of protein-protein interaction sites is essential for
      the mutant design and prediction of protein-protein networks. The
      interaction sites of residue units were predicted using support vector
      machines (SVM) and the profiles of sequentially/spatially neighboring
      residues, plus additional information. When only sequence information was
      used, prediction performance was highest using the feature vectors,
      sequentially neighboring profiles and predicted interaction site ratios,
      which were calculated by SVM regression using amino acid compositions.
      When structural information was also used, prediction performance was
      highest using the feature vectors, spatially neighboring residue profiles,
      accessible surface areas, and the with/without protein interaction sites
      ratios predicted by SVM regression and amino acid compositions. In the
      latter case, the precision at recall = 50% was 54-56% for a homo-hetero
      mixed test set and >20% higher than for random prediction. Approximately
      30% of the residues wrongly predicted as interaction sites were the
      closest sequentially/spatially neighboring on the interaction site
      residues. The predicted residues covered 86-87% of the actual interfaces
      (96-97% of interfaces with over 20 residues). This prediction performance
      appeared to be slightly higher than a previously reported study. Comparing
      the prediction accuracy of each molecule, it seems to be easier to predict
      interaction sites for stable complexes.
AD  - Department of Computational Biology, Graduate School of Frontier Science,
      The University of Tokyo, Kiban-3A1 (CB01), 1-5-1 Kashiwanoha Kashiwa,
      Chiba. akoike@hgc.jp
FAU - Koike, Asako
AU  - Koike A
FAU - Takagi, Toshihisa
AU  - Takagi T
LA  - eng
PT  - Journal Article
DEP - 20040120
PL  - England
TA  - Protein Eng Des Sel
JID - 101186484
SB  - IM
EDAT- 2004/03/30 05:00
MHDA- 2004/03/30 05:00
PHST- 2004/Jan/20 [aheadofprint]
AID - 10.1093/protein/gzh020 [doi]
AID - gzh020 [pii]
PST - ppublish
SO  - Protein Eng Des Sel 2004 Feb;17(2):165-73. Epub 2004 Jan 20