Biology – Quantitative Biology – Biomolecules
Scientific paper
2008-10-08
Structure, 17:234-246 (2009)
Biology
Quantitative Biology
Biomolecules
13 pages, 8 figures
Scientific paper
10.1016/j.str.2008.11.009
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and universality of ligand binding sites in protein structures, we conducted the all-against-all atomic-level structural comparison of over 180,000 ligand binding sites found in all the known structures in the Protein Data Bank by using a recently developed database search and alignment algorithm. By applying a hybrid top-down-bottom-up clustering analysis to the comparison results, we determined approximately 3000 well-defined structural motifs of ligand binding sites. Apart from a handful of exceptions, most structural motifs were found to be confined within single families or superfamilies, and to be associated with particular ligands. Furthermore, we analyzed the components of the similarity network and enumerated more than 4000 pairs of ligand binding sites that were shared across different protein folds.
Kinjo Akira R.
Nakamura Haruki
No associations
LandOfFree
Comprehensive structural classification of ligand binding motifs in proteins does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Comprehensive structural classification of ligand binding motifs in proteins, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Comprehensive structural classification of ligand binding motifs in proteins will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-29402