CRNPRED: Highly Accurate Prediction of One-dimensional Protein Structures by Large-scale Critical Random Networks

Details CRNPRED: Highly Accurate Prediction of One-dimensional Protein Structures by Large-scale Critical Random Networks CRNPRED: Highly Accurate Prediction of One-dimensional Protein Structures by Large-scale Critical Random Networks

2006-04-12

arxiv.org/abs/q-bio/0604013v1

BMC Bioinformatics, 7:401 (2006)

Biology

Quantitative Biology

Biomolecules

10 pages, 1 figure, 2 tables

Scientific paper

10.1186/1471-2105-7-401

Background: One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure relationship. Accurate prediction methods will serve as a basis for these and other purposes. Results: We implemented a program CRNPRED which predicts secondary structures, contact numbers and residue-wise contact orders. This program is based on a novel machine learning scheme called critical random networks. Unlike most conventional one-dimensional structure prediction methods which are based on local windows of an amino acid sequence, CRNPRED takes into account the whole sequence. CRNPRED achieves, on average per chain, Q3 = 81% for secondary structure prediction, and correlation coefficients of 0.75 and 0.61 for contact number and residue-wise contact order predictions, respectively. Conclusion: CRNPRED will be a useful tool for computational as well as experimental biologists who need accurate one-dimensional protein structure predictions.

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