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Conformational Ensembles from Experimental Data
and Computer Simulations
Poster Abstracts
48
15-POS
Board 15
CABS-flex Web Server for Fast Simulations of Flexibility of Globular Proteins
Maciej Ciemny
2,1
, Karolina Dawid
2,1
, Mateusz Kurcinski
1
, Maciej Blaszczyk
1
, Andrzej
Kolinski
1
, Sebastian Kmiecik
1
.
1
University of Warsaw, Warsaw, Poland,
2
University of Warsaw, Warsaw, Poland.
Investigating of the conformational flexibility of protein structures is crucial for understanding
their functions. Large timescales of protein molecular motions limit the applicability of standard
molecular dynamics methods to this problem. Our method - CABS-flex
1,2
– implements a highly
efficient, coarse-grained approach for prediction of fluctuations of the protein structures. The
resulting structural ensembles reflect the flexibility of investigated protein and provide a picture
complementary to the results obtained from molecular dynamics simulations
3
as well as NMR
conformational ensembles
2
. The CABS-flex methodology is also successfully used for efficient
simulations of protein flexibility in predictions of protein-peptide complexes
4,5
and protein
aggregation properties
6
. The CABS-flex web server is freely available at:
http://biocomp.chem.uw.edu.pl/CABSflex/.References:
1 Jamroz, M., Kolinski, A. & Kmiecik, S. CABS-flex: Server for fast simulation of protein
structure fluctuations. Nucleic Acids Res 41, W427-431, doi:10.1093/nar/gkt332 (2013).
2 Jamroz, M., Kolinski, A. & Kmiecik, S. CABS-flex predictions of protein flexibility compared
with NMR ensembles. Bioinformatics 30, 2150-2154, doi:10.1093/bioinformatics/btu184 (2014).
3 Jamroz, M., Orozco, M., Kolinski, A. & Kmiecik, S. Consistent View of Protein Fluctuations
from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based
Force-Field. J Chem Theory Comput 9, 119-125, doi:10.1021/ct300854w (2013).
4 Ciemny, M. P. et al. Protein-peptide molecular docking with large-scale conformational
changes: the p53-MDM2 interaction. Sci Rep 6, 37532, doi:10.1038/srep37532 (2016).
5 Ciemny, M., Kurcinski, M., Kozak, K., Koliński, A. & Kmiecik, S. in Methods in Molecular
Biology Vol. 1561 69-94 (2017).
6 Zambrano, R. et al. AGGRESCAN3D (A3D): server for prediction of aggregation properties of
protein structures. Nucleic Acids Res 43, W306-313, doi:10.1093/nar/gkv359 (2015).