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
) 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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