@article {264, title = {Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics}, journal = {International Journal of Molecular Sciences}, volume = {14}, year = {2013}, pages = {9893{\textendash}9905}, abstract = {We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.}, keywords = {coarse-grained modeling, molecular dynamics, multiscale modeling, protein dynamics}, issn = {1422-0067}, doi = {10.3390/ijms14059893}, url = {http://www.mdpi.com/1422-0067/14/5/9893}, author = {Jacek Wabik and Sebastian Kmiecik and Dominik Gront and Maksim Kouza and Andrzej Koli{\'n}ski} } @article {Kmiecik2012, title = {From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A}, journal = {The Journal of Physical Chemistry B}, volume = {116}, number = {23}, year = {2012}, month = {jun}, pages = {7026{\textendash}32}, abstract = {Atomic-level molecular dynamics simulations are widely used for the characterization of the structural dynamics of proteins; however, they are limited to shorter time scales than the duration of most of the relevant biological processes. Properly designed coarse-grained models that trade atomic resolution for efficient sampling allow access to much longer time-scales. In-depth understanding of the structural dynamics, however, must involve atomic details. In this study, we tested a method for the rapid reconstruction of all-atom models from $\alpha$ carbon atom positions in the application to convert a coarse-grained folding trajectory of a well described model system: the B domain of protein A. The results show that the method and the spatial resolution of the resulting coarse-grained models enable computationally inexpensive reconstruction of realistic all-atom models. Additionally, by means of structural clustering, we determined the most persistent ensembles of the key folding step, the transition state. Importantly, the analysis of the overall structural topologies suggests a dominant folding pathway. This, together with the all-atom characterization of the obtained ensembles, in the form of contact maps, matches the experimental results well.}, keywords = {coarse-grained modeling, molecular dynamics, multiscale modeling, protein dynamics}, issn = {1520-5207}, doi = {10.1021/jp301720w}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22486297}, author = {Sebastian Kmiecik and Dominik Gront and Maksim Kouza and Andrzej Koli{\'n}ski} }