Bioinformatics Vol. 16 no. 11 2000
Pages 978-987
© 2000 Oxford University Press
Original Paper |
Estimating the significance of sequence order in protein secondary structure and prediction
1 The European Bioinformatics Institute,
EMBL Outstation, Cambridge CB10 1SD, UK
2 Genetics, Harvard Medical School, 200
Longwood Avenue, Boston, MA 02115, USA
Received on November 3, 1999
; revised on April 24, 2000
; accepted on June 20, 2000
Motivation: How critical is the sequence order information in predicting protein secondary structure segments? We tried to get a rough insight on it from a theoretical approach using both a prediction algorithm and structural fragments from Protein Databank (PDB).
Results: Using reverse protein sequences and PDB structural fragments, we theoretically estimated the significance of the order for protein secondary structure and prediction. On average: (1) 79% of protein sequence segments resulted in the same prediction in both normal and reverse directions, which indicated a relatively high conservation of secondary structure propensity in the reverse direction; (2) the reversed sequence prediction alone performed less accurately than the normal forward sequence prediction, but comparably high (2% difference); (3) the commonly predicted regions showed a slightly higher prediction accuracy (4%) than the normal sequences prediction; and (4) structural fragments which have counterparts in reverse direction in the same protein showed a comparable degree of secondary structure conservation (73% identity with reversed structures on average for pentamers).
Contact: jong{at}biosophy.org; dietmann{at}ebi.ac.uk; heger{at}ebi.ac.uk; holm{at}ebi.ac.uk
*** Present address: EBI, Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. To whom correspondence should be addressed.