Integrating Web Resources to Model Protein Structure and Function

• Published in: Reasoning Web pp. 184 - 196
• Main Author: Krippahl, Ludwig
• Format: Book Chapter
• Language: English
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 2006
• Series: Lecture Notes in Computer Science
• Subjects: Model Protein Structure; Nucleic Acid Research; Protein Chain; Protein Data Bank; Simple Object Access Protocol
• ISBN: 9783540384090; 354038409X
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/11837787_8

In this paper we address computational aspects of protein structure and function, including prediction of secondary structure, folding, structure determination from Nuclear Magnetic Resonance data, modelling of protein interactions, and metabolic pathways. The subject is introduced with an overview of protein structure and chemistry and the algorithms and representations used to model protein structures. The main focus of the paper is the integration of information from sources relevant to protein structure modelling, such as structure databases and modelling servers, a task made difficult by the heterogeneity of formats, the diversity of data sources, and the sheer volume of information available, making evident the need for a standard framework for data sharing, i.e. the Semantic Web. To help solve this problem, we present tools being developed according to the concept of a Semantic Web. These include the UniProtRDF project and tools currently implemented on the Chemera molecular modelling software which can facilitate the search and application of information available from Internet servers and databases.