Abstract
Most of the biological processes are governed through specific protein–ligand interactions. Discerning different components that contribute toward a favorable protein– ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of ∼68 000 protein–ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein–ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein–ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database—protein–ligand interaction clusters (PLIC).Database URL: http://proline.biochem.iisc.ernet.in/PLIC
Highlights
Protein–ligand interactions play a vital role in all biological processes ranging from metabolic enzyme catalysis to regulation of complex signaling cascades
The large-scale structural information available on protein–ligand complexes has led to the development of various computational approaches that analyze protein–ligand interactions in terms of different attributes such as atomic contacts, binding energetics and shape recognition features
These attributes can be roughly divided into binding site properties of the protein, protein–ligand atomic contacts and different components of binding energetics involved in the interaction
Summary
Protein–ligand interactions play a vital role in all biological processes ranging from metabolic enzyme catalysis to regulation of complex signaling cascades. These attributes can be roughly divided into binding site properties of the protein, protein–ligand atomic contacts and different components of binding energetics involved in the interaction. We present a database providing the Protein Data Bank (PDB)-scale information of all similar binding sites for each protein–ligand complex.
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