Prediction of protein secondary structure based on residue pairs

J Bioinform Comput Biol. 2004 Jun;2(2):343-52. doi: 10.1142/s0219720004000594.

Abstract

The GOR program for predicting protein secondary structure is extended to include triple correlation. A score system for a residue pair to be at certain conformation state is derived from the conditional weight matrix describing amino acid frequencies at each position of a window flanking the pair under the condition for the pair to be at the fixed state. A program using this score system to predict protein secondary structure is established. After training the model with a learning set created from PDB_SELECT, the program is tested with two test sets. As a method using single sequence for predicting secondary structures, the approach achieves a high accuracy near 70%.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Cluster Analysis
  • Models, Molecular*
  • Models, Statistical
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Sequence Homology, Amino Acid

Substances

  • Amino Acids
  • Proteins