Protein engineering is employed in fields as diverse as animal nutrition, aquaculture, crop production, biofuels, biopharmaceuticals, food and beverages, household care, leather and textile, waste water solutions, and through chemical biology in the production of high-value chemical compounds. In recent years chemical biology has gained prominence. Chemical biology is the branch of general protein engineering that is concerned with the use of modified enzymes for the production of interesting, high-value chemical compounds.
Protein engineering has been a research topic for more than 25 years, and throughout this period theory and application have gone hand-in-hand. The NewProt partners intend to keep working in this tradition in that they want to integrate and develop protein engineering software and databases in a regime that includes rigorous and continuous experimental validation. The NewProt project reflects on the KBBE.2011.3.6-01 call "Increasing the accessibility, usability and predictive capacities of bioinformatics tools for biotechnology applications". The NewProt partners intend to bring together the combined skills of two prominent academic protein engineering labs and eight SMEs with a high profile in a wide variety of complementary protein engineering branches to produce a self-service portal (SSP) for protein engineering software and databases. Predictive technologies will be experimentally validated. Software and databases will as much as possible be free or open source. The NewProt team has been carefully selected to consist of teams that provide the highest quality work in their area of expertise, and the areas of expertise that come together are highly complementary. All partners (academic and SME alike) will benefit from a well-functioning SSP. The academic partners are already used to always give public access to their results, but in NewProt also all SMEs have business models that flourish by openness.
Two academic groups and eight SMEs who all work on different aspects of protein engineering will collaborate and produce a website, called SSP, that combines a portal with an interactive workbench to provide users a self-service system for in silico protein engineering. SSP will give users access to a wide variety of protein engineering facilities and information systems, and will allow them to interactively work with a comprehensive set of well-integrated computational protein engineering tools. The databases that will be provided will be curated and the software and protocols will be experimentally validated. The portal will be solidly based in modern information technology and its usability for protein engineering and for use by software providers will be thoroughly validated.
The three main, measurable NewProt objectives are 1) the design and implementation of the actual portal with workbench; 2) the comprehensive suite of fully interoperable, well-documented software, databases, and information system; and 3) the experimental results of the mutation and design experiments that will be executed to validate the software.
The validation experiments will additionally enable the protein engineering of synthetically useful enzymes and the engineered biocatalysts will be marketed by the SMEs Ingenza and Enzymicals. NewProt thus provides both SMEs with highly efficient tools to ensure an excellent and competitive standing in their business areas.
The final product of the project will be a series of experimentally validated well-documented protein engineering software facilities and protocols that will be made available for interactive use at a portal with an embedded workbench, called SSP, that is solidly rooted in modern information technologies. The SSP will be hosted at the CMBI, and will be freely accessible. The whole SSP will be made such that it can be downloaded for hosting and for in-house usage by third parties.