Comprehensive structural classification of ligand-binding motifs in proteins.

By Akira R. Kinjo, Haruki Nakamura. 2008

51 citations recorded by the source corpus.

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 structural motifs that were shared across different protein folds.

Subfields: Computational Theory and Mathematics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. L. Varshney
2. Dusanka Janezic
3. Janez Konc
4. Jesse Vig
5. Richard Socher
6. Caiming Xiong

In Molecular Biology

1. Ali Madani
2. L. Varshney
3. Dusanka Janezic
4. Janez Konc
5. Juyong Lee
6. Jesse Vig
7. Richard Socher
8. Caiming Xiong

Citations in the corpus

• BERTology Meets Biology: Interpreting Attention in Protein Language Models (2020, background): “Past work has shown that binding sites can reveal evolutionary relationships among proteins [42] and that particular structural motifs in binding sites are mainly restricted to specific families or superfamilies of proteins [37].”
• Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins (2017, background): “Our analysis is the first study that identified the similarities between the communities of binding sites compared to previous PDB-wide binding site analyses 13, 14 .”