PHD--an automatic mail server for protein secondary structure prediction

Comput Appl Biosci. 1994 Feb;10(1):53-60. doi: 10.1093/bioinformatics/10.1.53.


By the middle of 1993, > 30,000 protein sequences has been listed. For 1000 of these, the three-dimensional (tertiary) structure has been experimentally solved. Another 7000 can be modelled by homology. For the remaining 21,000 sequences, secondary structure prediction provides a rough estimate of structural features. Predictions in three states range between 35% (random) and 88% (homology modelling) overall accuracy. Using information about evolutionary conservation as contained in multiple sequence alignments, the secondary structure of 4700 protein sequences was predicted by the automatic e-mail server PHD. For proteins with at least one known homologue, the method has an expected overall three-state accuracy of 71.4% for proteins with at least one known homologue (evaluated on 126 unique protein chains).

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Biological Evolution
  • Computer Communication Networks
  • Databases, Factual
  • Molecular Sequence Data
  • Neural Networks, Computer
  • Office Automation*
  • Protein Structure, Secondary*
  • Proteins / chemistry
  • Proteins / genetics
  • Sequence Alignment / methods*


  • Proteins