Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 3

protein structure Related Publications

3 Detecting Community Structure in Amino Acid Interaction Networks

Authors: Omar GACI, Stefan BALEV, Antoine DUTOT

Abstract:

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we observe that according to their structural roles, the nodes interact differently. By leading a community structure detection, we confirm this specific behavior and describe thecommunities composition to finally propose a new approach to fold a protein interaction network.

Keywords: protein structure, interaction network, community structure detection

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1185
2 Introducing Sequence-Order Constraint into Prediction of Protein Binding Sites with Automatically Extracted Templates

Authors: Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, Darby Tien-Hao Chang

Abstract:

Search for a tertiary substructure that geometrically matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work, a web server has been built to predict protein-ligand binding sites based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for querying the library. The sequence-order constraint is employed to identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.

Keywords: protein structure, binding site, functional prediction

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1143
1 A General Model for Amino Acid Interaction Networks

Authors: Omar GACI, Stefan BALEV

Abstract:

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.

Keywords: protein structure, small-world network, interaction network

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1253