About

This is a collaboration between the the Scientific Data Analysis Lab of the Pervasive Technology Labs of Indiana University and the Mooney Laboratory in the Buck Institute. We currently support two tools for analysis through Web services, the S-BLEST method and mutation structural annotations. We have developed clients that are plugins for use in two well-developed molecular graphics tools: Delano Scientific's PyMOL and UCSF's Chimera.

Our Mission

Most of the LifeScienceWeb software is based on of our suite of Web Services. We encourage developers to take advantage of these Web Services in hopes it will aid research. Our goal is to create an active community to shape and grow our current feature set to include many more useful tools for the Life Sciences. We are excited about developers who are interested in extending their own tools to interact with our services. We will add services in (for beta testing) as they become available.

Web Services

We currently support two tools for analysis through Web services, the S-BLEST method and mutation structural annotations. We have developed plugins for Delano Scientific's PyMOL software and UCSF Chimera to take advantage of these services. The plugins are bundled together and can be downloaded here. For more information on the tools, click on the appropriate software link on the left.a

How Does It Work?

Upon installation of the web service a user has access to structurally annotated mutation data, and all structures and annotations are dynamically displayed based on the user's input. The user is not required to type advanced display commands, because the client leverages the power of all the services previously mentioned.

The visualization plugins allow for interactive exploration of the data. For example, in Chimera, once the plugin is installed, a new pull down submenu will appear under "Tools" labeled "LSW Services".

MutDB

SelectingI MutDB option under LSW Services in the menu options will bring up the MutDB controller. Several queries are possible here. First, and most easily, the user can enter the gene symbol, such as BRCA1, TP53, or AR. This will query the service and display the PDB IDs that are associated with that gene symbol. Upon selection of a PDB and chain ID, the chain is downloaded by our PDB chain service and the mutation positions are highlighted upon the resulting structure in red. Additionally, a list of the mapped nonsynonymous SNPs and mutations are displayed in the mutation list box. When the user selects a position from this box, the mutation is highlighted on the structure and the source accession number, PubMed ID, and comments are displayed in the information box. License
We offer commercial/private access to structurally annotated SNPs from dbSNP. Please contact Sean Mooney,

S-Blest

The Structure-Based Local Environment Search Tool uses vectors of amino acid structural environments to perform K Nearest Neighbor queries against a database of protein structures. Our Web services allow for authenticated (password protected) submission of a protein structure, or selection of an existing structure and searching it against common databases and then visualization of the results using UCSF Chimera or PyMOL. Currently the databases include ASTRAL 40 v1.67, ASTRAL 90 v1.67, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. License
The S-BLEST service requires a significant investment of our computer time, for commercial use we require a license agreement. Please contact Sean Mooney.

Disclaimer

URTC, the Mooney Lab and the Pervasive Technology Labs make no representations and extends no warranties of any kind, either express or implied. There are no express or implied warranties of merchantability or fitness of LSW Web Services for a particular purpose, or that the use of LSW Web Services will not infringe any patent, copyright, trademark, trade secret, or other intellectual property rights of another party, or any other express or implied warranties. IURTC will not be lieable to a user for any claims or damages arising from user's use of LSW Web Services, any claim for any loss or interruption of business, or for any indirect, special, or consequential damages of any kind.