Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices

• Type: Article in International Scientific Journal
• Date: 2008

Authors

Cristian Robert Munteanu (Author) Other; Humberto Gonzalez Diaz (Author) Other; Alexandre L Magalhaes (Author) FCUP

Journal

Title: Journal of Theoretical Biology

Vol. 254 No. 2

Pages: 476-482

ISSN: 0022-5193

Publisher: Elsevier

Indexing

ISI Web of Knowledge - 66 Citations

Scopus - 69 Citations

Scientific classification

FOS: Natural sciences > Mathematics

Other information

Authenticus ID: P-003-W4X

DOI: 10.1016/j.jtbi.2008.06.003

Abstract (EN): The huge amount of new proteins that need a fast enzymatic activity characterization creates demands of protein QSAR theoretical models. The protein parameters that can be used for an enzyme/non-enzyme classification includes the simpler indices such as composition, sequence and connectivity, also called topological indices (TIs) and the computationally expensive 3D descriptors. A comparison of the 3D versus lower dimension indices has not been reported with respect to the power of discrimination of proteins according to enzyme action. A set of 966 proteins (enzymes and non-enzymes) whose structural characteristics are provided by PDB/DSSP files was analyzed with Python/Biopython scripts, STATISTICA and Weka. The list of indices includes, but it is not restricted to pure composition indices (residue fractions), DSSP secondary structure protein composition and 3D indices (surface and access). We also used mixed indices such as composition-sequence indices (Chou's pseudoamino acid compositions or coupling numbers), 31)-composition (surface fractions) and DSSP secondary structure amino acid composition/propensities (obtained with our Prot-2S Web too[). In addition, we extend and test for the first time several classic TIs for the Randic's protein sequence Star graphs using our Sequence to Star Graph (S2SG) Python application. All the indices were processed with general discriminant analysis models (GDA), neural networks (NN) and machine learning (ML) methods and the results are presented versus complexity, average of Shannon's information entropy (Sh) and data/ method type. This study compares for the first time all these classes of indices to assess the ratios between model accuracy and indices/model complexity in enzyme/non-enzyme discrimination. The use of different methods and complexity of data shows that one cannot establish a direct relation between the complexity and the accuracy of the model.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 7