PDBeMotif is an extremely fast and powerful search tool that facilitates exploration of the Protein Data Bank (PDB) by combining protein sequence, chemical structure and 3D data in a single search. Currently it is the only tool that offers this kind of integration at this speed. PDBeMotif can be used to examine the characteristics of the binding sites of single proteins or classes of proteins such as Kinases and the conserved structural features of their immediate environments either within the same specie or across different species. For example, it can highlight a conserved activation loop common to protein kinases, which is important in regulating activity and is marked by conserved DFG and APE motifs at the start and end of the loop, respectively. The prediction of the effect of modifications to small molecules that bind to the active and/or regulatory sites of proteins on their efficacy can be based on the outcome of analytic work done using PDBeMotif.

   It can be ported to all major operating system platforms such as MS Windows, LINUX, Apple Mac and Solaris as it is written in Java and uses Oracle and the free source PostGreSQL database server. PDBeMotif can be used online or downloaded and installed locally where public and private PDB files (including libraries of theoretically derived 3D structures) can be loaded and analysed. There is also the capability to load protein site annotations, families and domains from Distributed Annotation System (DAS) servers.

Getting started:

The interface uses top tabs metaphor. The front page shows the following tabs:

• Search - for combining one or more criteria based on parameters such as single molecules or their chemical substructures, sequences of amino acids, sequence motifs, 3D structural motifs, sequences of dihedral angles (phi/psi), sequences of secondary structure elements (helixes, strands and loops) and text searches.
• PDB header search - for picking PDB entry using text search like by keywords, authors. The found entry can be viewed with respect of motifs and ligand interactions and be used to search fragmens of its structure in the PDB archive.
• Upload PDB file - for getting sites, motifs and ligand interactions annotation for a given coordinate file as well as using the interface provided to form a search criteria based on the structure.
• Molecule binding - for gathering and displaying ligand and other molecules or their fragments binding statistics with respect of protein and nucleotide residues, PROSITE motifs, small 3D structural motifs and secondary structure elements.
• Pair bonds - for gathering and displaying binding statistics where the bonds occur between the given pair of molecules or their fragments.
• Motif binding - for gathering and displaying PROSITE motif, small 3D motifs (beta-turn like) and secondary structure elements binding statistics with respect of ligand, protein and nucleotide residues, PROSITE motifs, small 3D structural motifs and secondary structure elements.
• 3D Environment - for gathering and displaying ligand 3D environment binding statistics. The 3D environment of a molecule is given by a set of residues whithout the sequence constraints on them. This interface answers the question : Which ligands bind the given environment and how often.
• Motif inclusion - for gathering and displaying motifs inclusion statistics. This statistics show how often one motif includes another. For instance, which small 3D structural motifs occur inside a PROSITE motif.

• PDB chemical search - for starting with a chemical substructure search in the PDB archive
• Submit a query in XML - XML query editor to search PDB
• Statistics query in XML - XML query editor to gather statistical data on PDB