Objective
The structure-based drug design (SBDD) and quantitative structure activity relationships (QSAR) approaches to lead discovery and optimisation are very valuable in drug design. They form the basis of the COMparative BINding Energy (COMBINE) analysis method which is a procedure to derive 3D-QSARs based on the structures of receptor-ligand complexes. COMBINE analysis has been applied to a range of systems including enzyme-inhibitor, enzyme-substrate, protein-protein and protein-DNA complexes. Unlike other 3D-Q SAR methodologies, COMBINE analysis can identify regions in the receptor important for binding specificity. However, the subsequent use of this information for optimising binding by ligand or receptor design is done by manual intervention. Our project aims to develop a software tool, COMBINE-ENGINEER, to automate this design task and embed it with a full iterative COMBINE analysis. It will thus provide an automated procedure for molecular design governed by protein structure based QSARs.
Specifically, COMBINE-ENGINEER will integrate:
1 COMBINE analysis to compute receptor-based 3D-QSARs;
2 Design of ligands and/or proteins to optimise binding as suggested by the COMBINE QSAR model. For proteins, this requires modelling of mutants, performing conformational searches and energetic optimisation. Existent techniques, such as side-chain conformations searching will be incorporated; For ligands, a virtual library of functional groups and a docking algorithm will be used to modify the known ligands;
3 Computation of COMBINE scores with the new- modelled complexes;
4 Iteration of points 2 and 3 to select the best molecules with optimal binding;
5 Additionally, further criteria, such as ADMET prediction and drug-like analysis, will be also considered.
The COMBINE-ENGINEER software will, as a whole, provide a package for system-specific lead optimisation in drug design and protein engineering applications.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences computer and information sciences software
- medical and health sciences basic medicine medicinal chemistry
- natural sciences biological sciences biochemistry biomolecules proteins
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Topic(s)
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
FP6-2004-MOBILITY-7
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Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
IIF - Marie Curie actions-Incoming International Fellowships
Coordinator
Germany
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.