Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions


Multiscale Modeling

"Thanks to enormous progress in sequencing of genomic data, presently we know millions of protein sequences. At the same time the number of experimentally solved protein structures is much smaller. This is because of large cost of structure determination. Thus, the theoretical in silico prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, and designing new technologies in the life science and material sciences. 


Unfortunately, a “brute force” approach remains impractical. Folding of a typical protein (in vivo or in vitro) takes milliseconds to minutes, while the state-of-the-art all-atom molecular mechanics simulations of protein systems can cover only a time period of nanoseconds to microseconds. This is the reason for the enormous progress in the development of various multiscale modeling techniques applied to protein structure prediction, modeling of protein dynamics and folding pathways, in silico protein engineering, model-aided interpretation of experimental data, modeling of macromolecular assemblies, and theoretical studies of protein thermodynamics. Coarse-graining of the proteins’ conformational space is a common feature of all these approaches, although the details and the underlying physical models span a very broad spectrum."


excerpt from the preface of "Multiscale Approaches to Protein Modeling" Andrzej Kolinski ed., Springer 2011 [read the full preface to the comprehensive review of multiscale modeling approaches]



Author(s): A.E. Badaczewska-Dawid; A. Koliński; S. Kmiecik
Computational and Structural Biotechnology Journal, 18:162-176, 2020
Author(s): M. Ciemny; A.E. Badaczewska-Dawid; M. Pikuzinska; A. Koliński; S. Kmiecik
International Journal of Molecular Sciences, 20:2019
Author(s): S. Kmiecik; M. Kouza; A. Dawid; A. Kloczkowski; A. Koliński
International Journal of Molecular Sciences, 19:2018
Author(s): S. Kmiecik; D. Gront; M. Kolinski; L. Wieteska; A. Dawid; A. Koliński
Chemical Reviews, 116:7898–7936, 2016
Author(s): J. Wabik; S. Kmiecik; D. Gront; M. Kouza; A. Koliński
International Journal of Molecular Sciences, 14:9893–9905, 2013
Author(s): S. Kmiecik; D. Gront; M. Kouza; A. Koliński
The Journal of Physical Chemistry B, 116:7026–32, 2012
Author(s): M. Kurcinski; M. Jamroz; A. Koliński
Multiscale Approaches to Protein Modeling, 21-34, 2011
Author(s): S. Kmiecik; M. Jamroz; A. Koliński; A. Koliński
Multiscale Approaches to Protein Modeling, 281-294, 2011
Author(s): S. Kmiecik; A. Koliński
Biophysical Journal, 94:726–36, 2008