Structural classification of protein binding regions for atomic comparative analysis of protein interactions


The main purpose of this server is to allow individual and comparative analysis of protein interactions. We have developed a structural classification of protein binding regions at family level based on the structural classification of proteins, SCOP. The user can easily navigate through the classification till the family of interest, where all the interacting information is collected. Three hierarchical interaction levels are defined: family, binding region and interface levels. The binding regions are defined as distinctive surface regions of a protein family used to recognize other molecules. The interfaces distinguish the different partners or ligands that a specific region can recognize. Ligands include proteins, peptides, nucleic acids and saccharides.

Click here to immediately start using SCOWLP.


Explore the different regions that the protein family "Heat-shock transcription factor" uses to recognize other molecules

  1. Type the name "Heat-shock transcription factor" in the search box. Two binding regions are shown: BR_1890 and BR_1891, where a different interacting pattern is shown in the alignment
  2. Click to visualize the differences in the binding surfaces and the information about the partners in the control panel. Click to download all pdb_chains complexes with the same binding region
  3. Click to predicted binding regions to get alternatives observed in proteins structurally similar to "Heat-shock transcription factor"

Identify a binding region that can recognize both, a protein and a DNA molecule

  1. Select in the search options for DNA "and" protein to filter the SCOP hierarchy for these families
  2. Navigate through the hierarchy, for instance: all alpha proteins » DNA/RNA binding 3-helical bundle » "Winged helix" DNA binding domain » Heat-shock transcription factor (TF) » BR_1892
  3. Interface IF_1893 corresponds to a TF homo-dimerization, whereas IF_1894 the TF interacts to DNA through the same region as it can be observed in both, the alignment pattern and the 3D viewer. Select any IF ID to visualize all interacting information for comparative analysis.

Identify all interacting information from a protein complex:

  1. Type a pdb file (1omw), all interaction between molecule pairs are shown, sorted out by family and binding region
  2. Select the domain binding region of interest (PH domain: BR_22689), you are redirected to the interface page, where it shows the different ligands that this region can recognize: Regulator of G protein signal, PH domain and BAR domain.
  3. Select the interface with RGS (IF_22690), all PH domains interacting to RGS are shown with the interaction pattern colored by water mediation or chemical type. Upon clicking a residue in the alignment it is highlighted in the 3D viewer and detailed interacting information is shown in the control frame.

References to SCOWLP:

  • Teyra J, Samsonov S, Schreiber S, Pisabarro MT. SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds. BMC Bioinformatics, 2011 Oct 13;12:398
  • Teyra J, Paszkowski-Rogacz M, Anders G, Pisabarro MT. SCOWLP classification: Structural comparison and analysis of protein binding regions. BMC Bioinformatics, 2008 Jan 8;9:9.
  • Teyra J, Doms A, Schroeder M, Pisabarro MT. SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. BMC Bioinformatics. 2006 Mar 2;7(1):104

References to SCOWLP usage:

  • Samsonov S, Teyra J, Anders G, Pisabarro MT. Analysis of the impact of solvent on contacts prediction in proteins. BMC Structural Biology, 2009 Apr 15;9:22.
  • Samsonov S, Teyra J, Pisabarro MT: A molecular dynamics approach to study the importance of solvent in protein interactions. Proteins. 2008 Nov 1;73(2):515-25.
  • Teyra J, Pisabarro MT. Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description. Proteins, 2007 Jun 1;67(4):1087-95.
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SCOWLP is based on SCOP 1.75.