Core 3: Structure-Function Linkage Database

Specific Aims

• Aim 1: Using the Enzyme Function Initiative (EFI) “Glue Grant to drive new technology for function assignment, develop and implement computational and bioinformatic tools and analyses to support creation of a general strategy for assignment of reaction and substrate specificity in functionally diverse enzyme superfamilies (SFs). The EFI is a driving biological project for the RBVI.
  • Aim 1A: Extend the SFLD schema and graphical user interface to support classification of sequences and structures into the appropriate SFs, subgroups, and monofunctional families for the five SFs used in the EFI as model systems. Each poses different challenges for curation, including variation in domain structures and other structural features, availability of genome/operon context, relative degree of available functional and mechanistic information, and the scientific challenges for inferring functions of unknowns. The goal of the EFI is to enable generalization of the functional assignment strategy to many additional superfamilies.
  • Aim 1B: Develop enhanced tools and protocols for updating, classifying, and analyzing structure-function relationships in these model superfamilies. Automate addition and preliminary curation of new sequences and structures as they are discovered in genome and metagenome projects. Collaborate with Core 1 to incorporate new Chimera tools and capabilities for interactive representation of structural information and sequence and structure analyses for SFLD SFs.
  • Aim 1C: Develop stable and robust interactions with the EFI Laboratory Information Management System, EFI Lab DB, to enable easy user access to EFI targets via the experimental data and information at Lab DB and the linked structure-function context for these targets at SFLD. Create and support search functions to enable users to access information in LabDB and SFLD in a transparent manner from the EFI homepage.
  • Aim 1D: Contribute to the development and implementation of schema features and new tools to support search and analysis of in silico docking results obtained from crystal structures and homology models for EFI targets.
• Aim 2: Develop and implement new tools to support analysis of the breadth of functionally diverse SFs represented in the enzyme universe.
  • Aim 2A: In collaboration with Core 4, automate and extend current tools for generation and interactive visualization of protein similarity networks that can be associated with known reaction and substrate specificity and other types of orthogonal biological information to provide a context for hypothesis development about functions of unknowns. The tools will enable generation on a large scale summary networks for a large number of SFs at the superfamily, subgroup, and family levels.
  • Aim 2B: Collaborate with Core 4 in development of the SFLD loader to allow access to SFLD data and information directly from Cytoscape.
  • Aim 2C: Extend the SFLD schema and ontology to support curation of this larger enzyme SF universe.
• Aim 3: Develop and deploy new cheminformatic tools for comparison and analysis of substrates and other ligands and for enzymatic reactions and mechanisms in functionally diverse SFs
  • Aim 3A: Develop new tools and interactive representations of known partial and overall reactions represented in SFLD SFs. Develop tools to generate “chemical similarity networks.” In analogy to protein sequence and structure similarity networks, these tools will enable hierarchical classification of known substrates and other ligands for SFs in the SFLD. Automated protocols that are currently available for identification of SF-conserved substrate substructures will be extended for more automated use in creating these representations on a large scale.
  • Aim 3B: Extend tools we previously created to quantitate comparison of overall enzymatic reactions and mechanisms for the enzymes of known reaction in SFLD SFs .
  • Aim 3C: Extend the SFLD schema and ontology to incorporate curation of substrates and other ligands and overall reactions and mechanisms associated with characterized enzymes in SFLD SFs.
• Aim 4: Contribute to and support the use of the SFLD for dissemination of structure-function relationships and biological function in functionally diverse enzyme SFs.
  • Aim 4A: Develop web services for dissemination of network downloads for curated SF sequences, structures, substrate sets, and mechanisms as that information is available.
  • Aim 4B: Develop web services to support creation of SF networks to which user sequence(s) of interest have been added to provide context for annotation, discovery of misannotation, and guide experimental design for many applications in enzyme structure-function investigations and enzyme engineering.
  • Aim 4C: In collaboration with Core 4, develop a package of easy to use scripts to allow users to create their own networks for visualization via Cytoscape. Create tutorials and other help documents to enable users to effectively work with SFLD tools, results, and data.