PEBank: A database for protein engineering data

DESCRIPTIONprovided by applicantEngineered proteins such as therapeutic antibodiesspecialized enzymes for drug manufacturingand proteins used to identify new small molecule drugs are making significant contributions to improve health careProtein therapeutics alone represent a $billion market that is rapidly growing and has broad applications in the treatment of cancermetabolic diseasesand other disordersThese advances have been made possiblein partby the free and easy access to data in the form of nucleotide sequencesGenBankand protein structuresProtein Data BankPDBBoth of these databases have grown exponentially and continue to organize and structure data in a manner that would be hard for individual groups or companies to maintain on their ownA new type of data is emerging in the protein engineering community that is not stored in GenBank or the PDB engineered protein sequences and their associated experimental assay dataThe protein engineering community is at a relatively early stage of development compared to the sequence or structure determination communitiesThusthe time is ripe to develop a database to organize the data from protein engineering studies into a cohesive and comprehensive datasetWe will call this database PEBankIn Phase IPEBank development will includedrafting a specification for Versionwith feedback from representatives from GenBank and the PDBthat describes the types of data to be stored and lays out the organizational hierarchy of the dataimplementing a prototype of Versionof PEBank and garnering feedback from the protein engineering communityimplementing a cloud based version of PEBankandcreating web based utilities for depositingviewingand analyzing dataIn Phase IIwe will continue development of PEBank bycreating a version that will allow write privileges and hosting it on Amazon Web Servicesproviding support for PEBank usersdeveloping a secure limited access version of PEBank that will hold customer specific proprietary datadeveloping tools that will validate the intregrity of the data and policies to handle invalid datadeveloping web enabled search tools to extract data from PEBanktesting data deposit and viewingand making PEBank available to the academic communityanddeveloping advanced analysis tools for finding statistical correlations between various data elementsWe will also begin to use the analysis tools and PEBank data to optimize the predictive capability of our computational protein design softwarethis will include improving the underlying score functions and developing dynamic design tools that integrate database interrogation with the sequence optimization processWhen completePEBank will allow protein engineers around the world to access protein engineering data in a standard format that can be easily accessedsearchedand sharedthis data can be used to inform their designs and to develop more predictive protein design toolsthus accelerating the development of new and improved proteins for therapeuticdiagnosticand other health related applications