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IPM
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YEARS OLD

“School of Biological Sciences”

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Paper   IPM / Biological Sciences / 13245
School of Biological Sciences
  Title:   Impact of Residue Accessible Surface Area on the Prediction of Protein Secondary Structures
  Author(s): 
1 . A. Momen-Roknabadi.
2 . M. Sadeghi.
3 . H. Pezeshk.
4 . S. A. Marashi.
  Status:   Published
  Journal: BMC Bioinformatics
  No.:  1
  Vol.:  9
  Year:  2008
  Pages:   357
  Supported by:  IPM
  Abstract:
Background The problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested that amino acid relative solvent accessibility (RSA) might be an effective factor for increasing the accuracy of protein secondary structure prediction. Previous studies have either used a single constant threshold to classify residues into discrete classes (buries vs. exposed), or used the real-value predicted RSAs in their prediction method.
Results We studied the effect of applying different RSA threshold types (namely, fixed thresholds vs. residue-dependent thresholds) on a variety of secondary structure prediction methods. With the consideration of DSSP-assigned RSA values we realized that improvement in the accuracy of prediction strictly depends on the selected threshold(s). Furthermore, we showed that choosing a single threshold for all amino acids is not the best possible parameter. We therefore used residue-dependent thresholds and most of residues showed improvement in prediction. Next, we tried to consider predicted RSA values, since in the real-world problem, protein sequence is the only available information. We first predicted the RSA classes by RVP-net program and then used these data in our method. Using this approach, improvement in prediction was also obtained.
Conclusion The success of applying the RSA information on different secondary structure prediction methods suggest that prediction accuracy can be improved independent of prediction approaches. Thus, solvent accessibility can be considered as a rich source of information to help the improvement of these methods.

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