Data Mining for Protein Secondary Structure Prediction

Abstract

Accurate protein secondary structure prediction from the amino acid sequence is essential for almost all theoretical and experimental studies on protein structure and function. After a brief discussion of application of data mining for optimization of crystallization conditions for target proteins we show that data mining of structural fragments of proteins from known structures in the protein data bank (PDB) significantly improves the accuracy of secondary structure predictions. The original method was proposed by us a few years ago and was termed fragment database mining (FDM) (Cheng H, Sen TZ, Kloczkowski A, Margaritis D, Jernigan RL (2005) Prediction of protein secondary structure by mining structural fragment database. Polymer 46:4314–4321). This method gives excellent accuracy for predictions if similar sequence fragments are available in our library of structural fragments, but is less successful if such fragments are absent in the fragments database. Recently we have improved secondary structure predictions further by combining FDM with classical GOR V (Kloczkowski A, Ting KL, Jernigan RL, Garnier J (2002a) Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins 49:154–66; Sen TZ, Jernigan RL, Garnier J, Kloczkowski A (2005) GOR V server for protein secondary structure prediction. Bioinformatics 21:2787–8) predictions to form a combined method, so-called consensus database mining (CDM) (Sen TZ, Cheng H, Kloczkowski A, Jernigan RL (2006) A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining. Protein Sci 15:2499–506). FDM mines the structural segments of PDB, and utilizes structural information from the matching sequence fragments for the prediction of protein secondary structures. By combining it with the GOR V secondary structure prediction method, which is based on information theory and Bayesian statistics, coupled with evolutionary information from multiple sequence alignments (MSA), our CDM method guarantees improved accuracies of prediction. Additionally, with the constant growth in the number of new protein structures and folds in the PDB, the accuracy of the CDM method is clearly expected to increase in future. We have developed a publicly available CDM server (Cheng H, Sen TZ, Jernigan RL, Kloczkowski A (2007) Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM). Bioinformatics 23:2628–30) (http://gor.bb.iastate.edu/cdm) for protein secondary structure prediction.