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Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship
- Source :
- Protein Science, Protein Science, Wiley, 2002, 11 (12), pp.2871-86
- Publication Year :
- 2002
- Publisher :
- HAL CCSD, 2002.
-
Abstract
- FREE FULL TEXT http://www.proteinscience.org/cgi/content/full/11/12/2871; Protein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 Calpha long. They make it possible to approximate and correctly predict local protein three-dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the amino acids in them and provide a good structural approximation for residues (i.e., sequences) 9 Calpha long. We present most of them in a simple network that describes 90% of the overall residues and, interestingly, includes more than 80% of the amino acids present in coils. Analysis of the network shows the specificity and quality of the 3D descriptions as well as a new type of relation between local folds and amino acid distribution. The results show that the 3D structure of these protein data banks can be easily described by a combination of subgraphs included in the network. Finally, a Bayesian probabilistic approach improved the prediction rate by 4%.
- Subjects :
- Models, Molecular
MESH: Databases, Protein
Relation (database)
Protein Conformation
MESH: Bayes Theorem
030303 biophysics
Bayesian probability
Molecular Sequence Data
MESH: Thermus thermophilus
Methionine-tRNA Ligase
MESH: Amino Acid Sequence
Biology
Type (model theory)
Biochemistry
Article
03 medical and health sciences
MESH: Protein Conformation
MESH: Computer Simulation
Simple (abstract algebra)
MESH: Methionine-tRNA Ligase
[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology
Computer Simulation
[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Amino Acid Sequence
Databases, Protein
MESH: Peptide Fragments
Molecular Biology
030304 developmental biology
chemistry.chemical_classification
0303 health sciences
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
MESH: Molecular Sequence Data
Thermus thermophilus
Probabilistic logic
Computational Biology
Bayes Theorem
Extension (predicate logic)
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Peptide Fragments
Amino acid
Crystallography
chemistry
Cover (topology)
Thermodynamics
MESH: Thermodynamics
Algorithm
MESH: Models, Molecular
MESH: Computational Biology
Subjects
Details
- Language :
- English
- ISSN :
- 09618368 and 1469896X
- Database :
- OpenAIRE
- Journal :
- Protein Science, Protein Science, Wiley, 2002, 11 (12), pp.2871-86
- Accession number :
- edsair.doi.dedup.....edabd9207f01b28a1f6b6dc708359c0b