Graph-based Structural Patterns for PDB

Well defined biomacromolecular patterns such as binding sites between a region of a protein and a ligand regulate certain factors that make possible the origin of many important biological phenomena. GSP4PDB is a user-friendly web application that lets the users design, search and analyze structural patterns inside biomacromolecules in a graphic way. This application uses the Protein Data Bank (PDB) to obtain detailed structural information.

The program receives a graph-based pattern formed by graphic components that represent a ligand and the amino acids around it. The pattern also includes some associations that condition the structure: distances between the ligand and the amino acids, distances between amino acids, and sequence of amino acids in the chain.

The user can determine what type of ligand want to analyze and include fixed amino acids but also can include amino acids 'any'. They can take the value of any amino acid, although the user can restrict them to a specific classification according to their polarity.

Finally, the program looks for coincidences inside each macromolecule in the PDB. The results of the search are shown in textual form and graphically by a 3D viewer. This analysis allows comparing proteins, DNA or RNA where the structure exists and evaluating how the amino acids surround the ligand in each coincidence.