PEBank A database for protein engineering data

Award Information
Agency: Department of Health and Human Services
Branch: National Institutes of Health
Contract: 4R44GM117961-02
Agency Tracking Number: R44GM117961
Amount: $591,315.00
Phase: Phase II
Program: SBIR
Awards Year: 2017
Solicitation Year: 2015
Solicitation Topic Code: 400
Solicitation Number: PA15-269
Small Business Information
251 S LAKE AVE STE 910, Pasadena, CA, 91101-3022
DUNS: 883426434
HUBZone Owned: N
Woman Owned: N
Socially and Economically Disadvantaged: N
Principal Investigator
 BARRY OLAFSON
 (626) 844-7348
 barry.olafson@protabit.com
Business Contact
 BARRY OLAFSON
Phone: (626) 844-7348
Email: barry.olafson@protabit.com
Research Institution
N/A
Abstract
DESCRIPTION provided by applicant Engineered proteins such as therapeutic antibodies specialized enzymes for drug manufacturing and proteins used to identify new small molecule drugs are making significant contributions to improve health care Protein therapeutics alone represent a $ billion market that is rapidly growing and has broad applications in the treatment of cancer metabolic diseases and other disorders These advances have been made possible in part by the free and easy access to data in the form of nucleotide sequences GenBank and protein structures Protein Data Bank PDB Both 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 own A 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 data The protein engineering community is at a relatively early stage of development compared to the sequence or structure determination communities Thus the time is ripe to develop a database to organize the data from protein engineering studies into a cohesive and comprehensive dataset We will call this database PEBank In Phase I PEBank development will include drafting a specification for Version with feedback from representatives from GenBank and the PDB that describes the types of data to be stored and lays out the organizational hierarchy of the data implementing a prototype of Version of PEBank and garnering feedback from the protein engineering community implementing a cloud based version of PEBank and creating web based utilities for depositing viewing and analyzing data In Phase II we will continue development of PEBank by creating a version that will allow write privileges and hosting it on Amazon Web Services providing support for PEBank users developing a secure limited access version of PEBank that will hold customer specific proprietary data developing tools that will validate the intregrity of the data and policies to handle invalid data developing web enabled search tools to extract data from PEBank testing data deposit and viewing and making PEBank available to the academic community and developing advanced analysis tools for finding statistical correlations between various data elements We will also begin to use the analysis tools and PEBank data to optimize the predictive capability of our computational protein design software this will include improving the underlying score functions and developing dynamic design tools that integrate database interrogation with the sequence optimization process When complete PEBank will allow protein engineers around the world to access protein engineering data in a standard format that can be easily accessed searched and shared this data can be used to inform their designs and to develop more predictive protein design tools thus accelerating the development of new and improved proteins for therapeutic diagnostic and other health related applications PUBLIC HEALTH RELEVANCE Engineered proteins such as therapeutic antibodies specialized enzymes for drug manufacturing and proteins used to identify new small molecule drugs are making significant contributions to improve health care The goal of the proposed research is to create a comprehensive web enabled database called PEBank to store and organize the wealth of data that are generated by protein engineering projects PEBank will allow scientists around the world to access protein engineering data in a consistent format to inform their protein engineering projects and develop better methods for engineering proteins relevant to human health

* Information listed above is at the time of submission. *

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