Alternative approach to protein structure prediction based on sequential similarity of physical properties
| Autor: | Yanping Yin, S. Rackovsky, Yi He, Harold A. Scheraga |
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| Rok vydání: | 2015 |
| Předmět: |
Models
Molecular 0303 health sciences Multidisciplinary Multiple sequence alignment Sequence Homology Amino Acid Sequence analysis Molecular Sequence Data 030303 biophysics Computational Biology Proteins Biological Sciences Biology Protein structure prediction Physical property Physical Phenomena 03 medical and health sciences Protein sequencing Biochemistry Pairwise comparison Amino Acid Sequence Homology modeling Biological system Alignment-free sequence analysis 030304 developmental biology |
| Zdroj: | Proceedings of the National Academy of Sciences. 112:5029-5032 |
| ISSN: | 1091-6490 0027-8424 |
| DOI: | 10.1073/pnas.1504806112 |
| Popis: | The relationship between protein sequence and structure arises entirely from amino acid physical properties. An alternative method is therefore proposed to identify homologs in which residue equivalence is based exclusively on the pairwise physical property similarities of sequences. This approach, the property factor method (PFM), is entirely different from those in current use. A comparison is made between our method and PSI BLAST. We demonstrate that traditionally defined sequence similarity can be very low for pairs of sequences (which therefore cannot be identified using PSI BLAST), but similarity of physical property distributions results in almost identical 3D structures. The performance of PFM is shown to be better than that of PSI BLAST when sequence matching is comparable, based on a comparison using targets from CASP10 (89 targets) and CASP11 (51 targets). It is also shown that PFM outperforms PSI BLAST in informatically challenging targets. |
| Databáze: | OpenAIRE |
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