Discovering conserved 3D-patterns among protein structures may provide valuable insights into protein classification, functional annotations or rational drug design. Thus, several tools have been developed to compare 3D-patterns; however, most of them only consider the previously known 3D-patterns such as binding sites or structural motifs. This fact makes necessary the development of new methods for the identification of all possibles 3D-patterns available in protein structures (allosteric sites, enzyme-cofactor interaction motifs, among others). 3D-PP a new free access web server for discovering and recognition all similar 3D amino acid patterns among a set of proteins structures (independently of their sequence similarity). This tool does not require any previous knowledge about ligands or motifs. The input can be a text file with the PDB accession codes or a zip file of PDB coordinates regardless of the origin of the structural data: X-ray crystallographic experiments or in silico comparative modeling. Finally, the results are lists of sequence patterns that can be further analyses within the web page.
Original paper: Valdés-Jiménez A, Larriba-Pey JL, Núñez-Vivanco G, Reyes-Parada M. 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns. Int J Mol Sci. 2019;20(13):3174 doi: https://doi.org/10.3390/ijms20133174