Objective
Recent studies show that protein function is not only determined by the static folded three-dimensional structure, but also by the distribution of the populations of its conformational sub-states within different environments. A detailed investigation of interacting protein interfaces requires - beyond the knowledge of their structure - information about their flexibility and the range of accessible conformations of the native state and complexed states. Additionally, successful protein structure prediction has demonstrated the suitability of “building blocks” (prototype fragments) as embodiment of local biological and physicochemical features. It is expected that the overall dynamics of protein structures can similarly be assembled from fragment flexibilities embedded in a known protein fold. Therefore this proposal focuses on developing a fast fragment-based method to predict the dynamics of a native or designed protein structure, which will be used to determine or define function in interaction networks and binding specificity in protein-ligand complexes. Specifically, the dynamics of prototypical fragments from a representative protein set will be sampled by molecular simulations; a flexibility predictor will be designed, implemented using Hidden Markov Model (HMM) and trained on dynamic profiles of the prototypical fragments; by using the flexibility predictor protein-protein and protein-ligand interactions will be investigated. For protein-protein interactions the flexibility of all known high-resolution protein structures will be predicted and made publicly available. To study flexibility as determinant of ligand-binding specificity, comparisons between the conformational sub-space of protein-ligand complexes and the space of all accessible conformations of the unbound components will be performed.
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.
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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.
FP7-PEOPLE-2007-2-1-IEF
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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.
Coordinator
W1B 1AL LONDON
United Kingdom
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.