The JCSG high-throughput structural biology pipeline

Abstract

The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism. Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination. The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to-structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications.

Figure 1

PSI Network strategy for structural genomics. In PSI-2, a network of research and resource centers were assembled in order to address its central mission of structural coverage of unexplored regions of protein-sequence space. Achieving a better understanding of the relationships between protein sequence and structure represents a critically important challenge to address the PSI’s principal goal of making structural information of most proteins readily available from knowledge of their corresponding gene sequences.

Figure 2

JCSG high-throughput structural biology pipeline. A linear representation is shown, highlighting the typical flow of targets through the multiple processing stages in the JCSG pipeline. The pipeline is subdivided into four main processing stages: (i) target selection, (ii) protein production and biophysical analysis, (iii) structure determination and (iv) structure analysis, annotation and distribution to public databases.

Figure 3

Evolution of main pipeline workflow. Flowchart of the current JCSG HTSB pipeline highlighting feedback loops and salvage pathways for recalcitrant targets.

Figure 4

JCSG PSI-2 production pipeline and underlying data-handling architecture. The JCSG large-scale production center integrates custom and commercial instrumentation into the highly parallelized HTSB pipeline. Data capture from >500 parameters encompassing over 30 stages are captured to a centralized database via the JCSG tracking database that parallels the experimental pipeline. Data flow back to the experimental pipeline provides feedback for target and pipeline management and smart target selection.