Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session II

42 – POS Board 14 Implementation and Evaluation of the New Protocol for Protein Homology Modeling Marta Strumillo , Dominik Gront. LTB, Warsaw, Poland. Template-based modelling of a protein structure is one of ubiquitous tasks of structural bioinformatics. The methods can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-based modelling, which combines computational tools recently developed in the Laboratory of Theory of Biopolymers: database of protein domain structured (BDDB) with one dimensional and three dimensional threading. At the first stage, template domain structures are assigned to the a sequence by the means of 1D Threading approach. Then the query-template pairs are subjected to a 3D threading procedure where a Monte Carlo search scheme is used to search for lowest scoring alignments. Finally, a number of model structures are build based on each of the alignments. Three different methods are used for this purpose: Modeller, Rosetta and CABS to ensure proper handling of various modelling scenarios that range from very easy to most difficult cases where only a remote homology may be detected. The models are clustered including possibility of knotted structures and the final solution is selected. The protocol is currently tested in ongoing CASP11 experiment. Gniewek et al. BMC Bioinformatics 2014, 15:22 BioShell-Threading: versatile Monte Carlo package for protein 3D threading Gront et al. NAR, 2012, Vol. 40 BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles

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