%0 Journal Article %J Nucleic Acids Research %D 2013 %T CABS-flex: server for fast simulation of protein structure fluctuations %A Michal Jamroz %A Andrzej Koliński %A Sebastian Kmiecik %K molecular dynamics %K near-native dynamics %K protein dynamics %K protein flexibility %K simulation %X The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics-a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions. %B Nucleic Acids Research %V 41 %P W427-W431 %8 2013 May 8 %G eng %U http://nar.oxfordjournals.org/cgi/content/full/gkt332 %N W1 %R 10.1093/nar/gkt332 %0 Journal Article %J Journal of Chemical Theory and Computation %D 2013 %T Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field %A Michal Jamroz %A Modesto Orozco %A Andrzej Koliński %A Sebastian Kmiecik %K molecular dynamics %K near-native dynamics %K protein dynamics %K protein flexibility %K simulation %X It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution. %B Journal of Chemical Theory and Computation %V 9 %P 119 - 125 %8 12/2012 %@ 1549-9618 %G eng %U http://dx.doi.org/10.1021/ct300854w %N 1 %! J. Chem. Theory Comput. %R 10.1021/ct300854w