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 I

4 – POS Board 4 Modeling of Protein Structure and Flexibility using CABS-fold and CABS-flex Web Servers Maciej Blaszczyk , Michal Jamroz, Sebastian Kmiecik, Andrzej Kolinski. University of Warsaw, Warsaw, Poland. Recently, we developed automated modeling methods for efficient prediction of protein structure - CABS-fold - and protein flexibility - CABS-flex. Both methods have been made available as web servers (see http://biocomp.chem.uw.edu.pl/tools) and can be easily used in various protein modeling tasks. The CABS-fold [1] server provides tools for protein structure prediction from sequence only ( de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS [2] modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The CABS-flex [3] server provides an efficient modeling protocol for the fast simulations of near-native dynamics of globular proteins. The CABS-flex was shown to be a computationally efficient alternative to all-atom molecular dynamics - a classical simulation approach. Moreover, we demonstrated that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles [4]. References: 1. Blaszczyk, M., Jamroz, M., Kmiecik, S. and Kolinski, A. (2013) CABS-fold: server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Research, W406-11. 2. Kolinski, A. (2004) Protein modeling and structure prediction with a reduced representation. Acta biochimica Polonica, 51, 349-371. 3. Jamroz, M., Kolinski, A. and Kmiecik S. (2013) CABS-flex: Server for fast simulation of protein structure fluctuations. Nucleic Acids Research, W427-31. 4. Jamroz, M., Kolinski, A., and Kmiecik, S. (2014) CABS-flex predictions of protein flexibility compared with NMR ensembles. Bioinformatics, doi: 10.1093/bioinformatics/btu184.

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