ADDITION OF CONTACT NUMBER INFORMATION CAN IMPROVE PROTEIN SECONDARY STRUCTURE PREDICTION BY NEURAL NETWORKS

Prediction of protein secondary structures is one of the oldest problems in Bioinformatics. Although several different methods have been proposed to tackle this problem, none of these methods are perfect. Recently, it is proposed that addition of other structural information like accessible surface area of residues or prior information about protein structural class can sig- nificantly improve the prediction of secondary structures. In this work, we propose that con- tact number information can be considered as another useful source of information for im- provement of secondary structure prediction. Since contact number, i. e. the number of other amino acid residues in the structural neighbourhood of a certain residue, depends on the sec- ondary structure of the residue, we conjectured that contact number data can improve secon- dary structure prediction. We used two closely related neural networks to predict secondary structures. The only difference in the neural networks was that one of them was also provided with residue contact numbers as an additional input. Results suggested that addition of contact number information can result in a small, but significant improvement in prediction of secon- dary structures in proteins. Our results suggest that residue contact numbers can be used as a rich source of information for improvement of protein secondary structure prediction.

[1]  David S. Wishart,et al.  Improving the accuracy of protein secondary structure prediction using structural alignment , 2006, BMC Bioinformatics.

[2]  W. C. Johnson,et al.  Environment affects amino acid preference for secondary structure. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Xueling Li,et al.  Efficient ensemble schemes for protein secondary structure prediction. , 2008, Protein and peptide letters.

[4]  Aleksey A. Porollo,et al.  Combining prediction of secondary structure and solvent accessibility in proteins , 2005, Proteins.

[5]  C. Anfinsen,et al.  The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[6]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[7]  Hamid Pezeshk,et al.  Impact of residue accessible surface area on the prediction of protein secondary structures , 2008, BMC Bioinformatics.

[8]  Fadime Üney Yüksektepe,et al.  Prediction of secondary structures of proteins using a two-stage method , 2008, Comput. Chem. Eng..

[9]  B. Rost,et al.  Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.

[10]  Burkhard Rost,et al.  Rising Accuracy of Protein Secondary Structure Prediction , 2003 .

[11]  C Sander,et al.  On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[12]  P. S. Kim,et al.  Context-dependent secondary structure formation of a designed protein sequence , 1996, Nature.

[13]  Guoli Wang,et al.  PISCES: recent improvements to a PDB sequence culling server , 2005, Nucleic Acids Res..

[14]  Christodoulos A. Floudas,et al.  Advances in protein structure prediction and de novo protein design : A review , 2006 .

[15]  Alessandro Vullo,et al.  Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information , 2007, BMC Bioinformatics.

[16]  Hamid Pezeshk,et al.  Adaptation of proteins to different environments: a comparison of proteome structural properties in Bacillus subtilis and Escherichia coli. , 2007, Journal of theoretical biology.

[17]  Giovanni Colonna,et al.  Amino acid propensities for secondary structures are influenced by the protein structural class. , 2006, Biochemical and biophysical research communications.

[18]  Jitao Huang,et al.  Secondary structural wobble: the limits of protein prediction accuracy. , 2002, Biochemical and biophysical research communications.

[19]  Yaoqi Zhou,et al.  Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training , 2006, Proteins.

[20]  C. Anfinsen,et al.  Reductive cleavage of disulfide bridges in ribonuclease. , 1957, Science.

[21]  T L Blundell,et al.  The use of amino acid patterns of classified helices and strands in secondary structure prediction. , 1996, Journal of molecular biology.

[22]  Guoli Wang,et al.  PISCES: a protein sequence culling server , 2003, Bioinform..

[23]  Angelo M. Facchiano,et al.  PreSSAPro: A software for the prediction of secondary structure by amino acid properties , 2007, Comput. Biol. Chem..

[24]  White Fh,et al.  Regeneration of native secondary and tertiary structures by air oxidation of reduced ribonuclease. , 1961 .

[25]  S. Sudarsanam,et al.  Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations , 1998, Proteins.

[26]  W C Johnson,et al.  Environmental features are important in determining protein secondary structure , 2001, Protein science : a publication of the Protein Society.

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

[28]  Scott R. Presnell,et al.  Origins of structural diversity within sequentially identical hexapeptides , 1993, Protein science : a publication of the Protein Society.

[29]  D Baker,et al.  Global properties of the mapping between local amino acid sequence and local structure in proteins. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Yanqing Zhang,et al.  A New SVM-Based Decision Fusion Method Using Multiple Granular Windows for Protein Secondary Structure Prediction , 2008, RSKT.

[31]  C. Anfinsen,et al.  Studies on the reduction and re-formation of protein disulfide bonds. , 1961, The Journal of biological chemistry.

[32]  F. H. White.  Regeneration of native secondary and tertiary structures by air oxidation of reduced ribonuclease. , 1961, The Journal of biological chemistry.