A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes

In this paper we describe an algorithm, based on neural networks that adds to the previously published results (ISPRED, www.biocomp.unibo.it) and increases the predictive performance of protein-protein interaction sites in protein structures. The goal is to reduce the number of spurious assignment and developing knowledge based computational approach to focus on clusters of predicted residues on the protein surface. The algorithm is based on neural networks and can be used to highlight putative interacting patches with high reliability, as indicated when tested on known complexes in the PDB. When a smoothing algorithm correlates the network outputs, the accuracy in identifying the interaction patches increases from 73% up 76%. The reliability of the prediction is also increased by the application the smoothing procedure.

[1]  Chris Sander,et al.  The HSSP database of protein structure-sequence alignments and family profiles , 1998, Nucleic Acids Res..

[2]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[3]  Alfonso Valencia,et al.  Prediction of protein-protein interactions from evolutionary information. , 2003, Methods of biochemical analysis.

[4]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[5]  B. Rost,et al.  Conservation and prediction of solvent accessibility in protein families , 1994, Proteins.

[6]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[7]  Patrick Aloy,et al.  Interrogating protein interaction networks through structural biology , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Giulio Superti-Furga,et al.  Protein complexes and proteome organization from yeast to man. , 2003, Current opinion in chemical biology.

[9]  A. Valencia,et al.  Prediction of protein--protein interaction sites in heterocomplexes with neural networks. , 2002, European journal of biochemistry.

[10]  Huan‐Xiang Zhou,et al.  Prediction of protein interaction sites from sequence profile and residue neighbor list , 2001, Proteins.

[11]  T. Earnest,et al.  From words to literature in structural proteomics , 2003, Nature.

[12]  B. Schwikowski,et al.  A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.

[13]  S. Strogatz.  Exploring complex networks , 2001, Nature.

[14]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.