Enhancing UCSF Chimera through web services

Abstract

Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList.

Figure 1.

Chimera dialog showing results from BLAST-searching the sequences in the PDB with the query sequence UniProt Q16BX4. The results include multiple chains with the same PDB ID because the searching option to ‘List only best-matching chain per PDB entry’ was unchecked. Additional columns of information such as crystallographic resolution have been fetched from the RCSB PDB.

Figure 2.

Side-by-side comparison of the BLAST pseudo-MSA (left) and the MSA from Clustal Omega (right) of the query and chains A of 4N5W, 2ZZV, 2HZL, 4MCO and 2VPN. Each alignment is displayed in a Multalign Viewer window in Chimera. Residues within 5 A of the respective bound ligands are highlighted in yellow. Residues missing from the 3D structures are enclosed in red outline boxes. Clustal Omega was run using one iteration and full distance matrices during the initial alignment and iteration. Blue rectangles outline some of the places where binding-site residues in the template structures (yellow) are aligned differently with the query sequence, which would give rise to different binding-site residues in the resulting comparative models.

Figure 3.

The five template structures (top left), the Modeller input dialog (top right) and the resulting five comparative models (bottom) in Chimera. In the dialog, the query is designated as the target for comparative modeling, and 4N5W, 2ZZV, 2HZL, 4MCO and 2VPN are chosen as the templates. Structures are shown as ribbons, with ligands in the sphere representation. Template structure colors match the boxes around the sequence names in the previous figure, namely: 4N5W in tan, 2ZZV in light blue, 2HZL in light purple, 4MCO in light green and 2VPN in coral. The comparative models are white.