Effect of Secondary Structure Prediction on Protein Fold Recognition and Database Search

Hydrophobic long-range interactions and local polypeptide chain propensities are the major factors directing protein folding. Incorporating both these terms in addition to the Dayhoff matrix helps us to increase quality of protein fold recognition via sequencestructure alignment. We have shown that the results of secondary structure prediction substantially increase a sensitivity of the fold recognition . To measure a performance of the protein fold recognition, we have developed a comprehensive test along with a set of the quality control scores based on the most populated structural families . With this test we have demonstrated improvement of the sequence alignment with consideration of the predicted secondary structure, even without knowledge of the real three-dimensional structure.

[1]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.

[2]  M. Sippl.  Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.

[3]  P. Y. Chou,et al.  Empirical predictions of protein conformation. , 1978, Annual review of biochemistry.

[4]  A A Salamov,et al.  Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. , 1995, Journal of molecular biology.

[5]  D. Fischer,et al.  Protein fold recognition using sequence‐derived predictions , 1996, Protein science : a publication of the Protein Society.

[6]  G. Barton,et al.  Protein fold recognition by mapping predicted secondary structures. , 1996, Journal of molecular biology.

[7]  B. Rost,et al.  Combining evolutionary information and neural networks to predict protein secondary structure , 1994, Proteins.

[8]  E. Lander,et al.  Protein secondary structure prediction using nearest-neighbor methods. , 1993, Journal of molecular biology.

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

[10]  S. Wodak,et al.  Protein structure prediction by threading methods: Evaluation of current techniques , 1995, Proteins.

[11]  D. Eisenberg,et al.  A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.

[12]  O. Gotoh.  An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.

[13]  R Nussinov,et al.  Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.