The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

Abstract

The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org ) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI's high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology.

Fig. 1

Example of a structure result summary for (PDB + 3cqw). a Search results that contain structural matches will present an annotations panel and molecular visualization tool. b Hovering the mouse over the Chain ID will launch an annotations quick table, summarizing if popular resources have an annotation for the protein sequence in that structure’s chain. c All annotations are accessible from a “post-it” with biological subjects on it—clicking on any subject will take you directly to that page of the “annotations notebook”

Fig. 2

Example of a Protein Model Portal model comparison analysis. Two theoretical models of a DNA polymerase from mouse (UniProt + Q9QUG2) have been selected for further structural variability analysis by the PMP. a The graphical representation indicated the overlapping residue range that can be compared. b The superposition of the two models shows that ModBase (black) and Swiss-model (blue) predict a different structure on the left side of the depiction. c. A graph showing the local (per residue) deviation of individual models/structures from mean of the ensemble of models/structures based on a distance RMSD (dRMSD). d The colors of the spectrum indicate the degree of variability (based on a weighted dRMSD) among the structure models (blue = low, green = medium, red = high)

Fig. 3

Example of a Sequence Analysis report. The CNT system and SCA-tool will both perform an SBKB query on given sequences to find the number of similar structures, models, and targets. It will also submit the sequence to the PSI-developed XtalPred and Pxs servers to calculate biophysical parameters and crystallization propensities. In this example, the given sequence was calculated to be a class 4 difficulty (hard), so further construct optimization may be required to ensure a successful structure determination