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Computational toolbox for protein surface docking

Computational toolbox for protein surface docking

Objective

Recent combinatorial biotechnologies have shown that the molecular recognition capability of proteins can be specifically oriented toward inorganic surfaces. The use of technologies based on such specificity would give European industry a competitive edge in several emerging fields (from nanoelectronics over biomaterials science to drug design), spanning different thematic areas of FP6.

However, at present the principles regulating protein-surface interactions are poorly understood, thus hindering such technologies from taking off.

What features of the surface and of the proteins (electronic, structural, morphological) determine which protein is able to bind to a given surface and how?

PROSURF will answer this question and provide the European scientific/technological community with computational tools to enable rational design of protein-surface associations.

As automated in silico docking revolutionized the process of drug discovery, so the outcomes of PROSURF will open genuinely new routes to solve several urgent technological problems, such as self-assembly of nanoelectronic devices or design of highly biocompatible materials. PROSURF is risky because it addresses a largely unexplored subject; however, the risk is compensated by the potential of enormous impact.

Our strategy to probe the determinants of protein-surface specificity, and to implement the envisaged computational tools, integrates state-of-the-art computational techniques and experiments. It consists of a series of computational steps, including quantum-mechanics based parameterisation of protein-surface interactions, molecular dynamics simulation of proteins on surfaces, and the implementation of protein-surface docking software, corroborated by tailored experiments.

Although the project focus is on theory, feedback from experiments will be important both to validate the computational tools, and to gain new insight into the basis of protein-surface interactions.

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Coordinator

UNIVERSITA' DEGLI STUDI DI MODENA E REGGIO EMILIA

Address

Via Universita' 4
Modena

Italy

Administrative Contact

Participants (4)

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CONSIGLIO NAZIONALE DELLE RICERCHE

Italy

EML RESEARCH GGMBH

Germany

LUDWIG MAXIMILIANS UNIVERSITY MUENCHEN

Germany

WEIZMANN INSTITUTE OF SCIENCE

Israel

Project information

Grant agreement ID: 28331

  • Start date

    1 September 2006

  • End date

    31 December 2009

Funded under:

FP6-POLICIES

  • Overall budget:

    € 1 356 000

  • EU contribution

    € 1 000 000

Coordinated by:

UNIVERSITA' DEGLI STUDI DI MODENA E REGGIO EMILIA

Italy