Automatic generation of 3D motifs for classification of protein binding sites

Background: Since many of the new protein structures delivered by high-throughput processes do not have any known function, there is a need for structure-based prediction of protein function. Protein 3D structures can be clustered according to their fold or secondary structures to produce classes of some functional significance. A recent alternative has been to detect specific 3D motifs which are often associated to active sites. Unfortunately, there are very few known 3D motifs, which are usually the result of a manual process, compared to the number of sequential motifs already known. In this paper, we report a method to automatically generate 3D motifs of protein structure binding sites based on consensus atom positions and evaluate it on a set of adenine based ligands. Results: Our new approach was validated by generating automatically 3D patterns for the main adenine based ligands, i.e. AMP, ADP and ATP. Out of the 18 detected patterns, only one, the ADP4 pattern, is not associat...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Jean-Christophe Nebel, Pawel Herzyk, David R. Gilbert
• Keywords: Adenine Based Ligands, BMCBI 2007, Protein Structure, Proteins