Bioinformatics Bioinformatics Tool Structure Analysis


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PDBeMotif is a highly 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 online or downloaded and installed locally where public and private PDB files (including libraries of theoretically derived 3D structures) can be loaded and analyzed. There is also the capability to load protein site annotations, families and domains from Distributed Annotation System (DAS) servers.


  • It 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 species or across different species. 
  • 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.
  • The PDBe is also active in the maintenance of the PDB archive and runs a deposition system through which new macromolecular structures can be added to the archive.


  • 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. 
  • PDBe is actively working with the X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy and cryo-Electron Microscopy (EM) communities.
  • PDBe maintains collaborations with several other major bioinformatics projects hosted at the European Bioinformatics Institute (EBI) and around the world.

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. 

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. 

Motif inclusion for gathering and displaying motifs inclusion statistics. 


  • To expertly handle deposition and annotation of structural data as one of the wwPDB deposition sites. 
  • To provide an integrated resource of high-quality macromolecular structures and related data. This is implemented by developing and maintaining advanced structural bioinformatics databases and services that are or even define the state of the art. 
  • To maintain in-house expertise in all the major structure determination techniques (X-ray, NMR and EM) so as to be able to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (e.g. data representation, harvesting, formats and standards or validation of structural data).

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