@article {259, title = {CABS-flex: server for fast simulation of protein structure fluctuations}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, month = {2013 May 8}, pages = {W427-W431}, abstract = {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.}, keywords = {molecular dynamics, near-native dynamics, protein dynamics, protein flexibility, simulation}, issn = {1362-4962}, doi = {10.1093/nar/gkt332}, url = {http://nar.oxfordjournals.org/cgi/content/full/gkt332}, author = {Michal Jamroz and Andrzej Koli{\'n}ski and Sebastian Kmiecik} } @article {260, title = {Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field}, journal = {Journal of Chemical Theory and Computation}, volume = {9}, year = {2013}, month = {12/2012}, pages = {119 - 125}, abstract = {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.}, keywords = {molecular dynamics, near-native dynamics, protein dynamics, protein flexibility, simulation}, isbn = {1549-9618}, doi = {10.1021/ct300854w}, url = {http://dx.doi.org/10.1021/ct300854w}, author = {Michal Jamroz and Modesto Orozco and Andrzej Koli{\'n}ski and Sebastian Kmiecik} } @article {Vieth1995a, title = {A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations}, journal = {Journal of Chemical Physics}, volume = {102}, number = {April}, year = {1995}, pages = {6189{\textendash}6193}, abstract = {A combined Monte Carlo (MC) simulation-statistical mechanical treatment is proposed to calculate the internal partition function and equilibrium constant. The method has been applied to a number of one and multidimensional analytical functions. When sampling is incomplete, various factorization approximations for estimating the partition function are discussed. The resulting errors are smaller when the ratios of the partition functions are calculated (as in the determination of equilibrium constants) as opposed to the partition function itself. {\textcopyright} 1995 American Institute of Physics.}, keywords = {equilibrium, factorization, molecules, Monte Carlo Method, partition functions, simulation, statistical mechanics}, doi = {http://link.aip.org/link/doi/10.1063/1.469063}, url = {http://smartech.gatech.edu/handle/1853/27021}, author = {Michal Vieth and Andrzej Koli{\'n}ski and Jeffrey Skolnick} } @article {Rey1992, title = {Effect of double bonds on the dynamics of hydrocarbon chains}, journal = {Journal of Chemical Physics}, volume = {97}, year = {1992}, pages = {1240{\textendash}1249}, abstract = {Brownian dynamics simulations of isolated 18-carbon chains have been performed, both for saturated and unsaturated hydrocarbons. The effect of one or several (nonconjugated) double bonds on the properties of the chains is discussed in terms of both equilibrium and dynamic properties. The introduction of a cis double bond increases the relaxation rates of the unsaturated chain with respect to the saturated alkane. On the other hand, coupling effects in the torsional transitions around a trans double bond make the dynamics of this unsaturated chain very similar to the saturated one. Based on these results, the parameters and moves of a dynamic Monte Carlo algorithm are tuned to reproduce the observed behavior, providing an efficient method for the study of more complicated systems.}, keywords = {Algorithms, Brownian Movement, Chains, Coupling, Double Bonds, dynamics, equilibrium, Hydrocarbons, Monte Carlo Method, Relaxation, Saturation, simulation, Torsion}, doi = {10.1063/1.463250}, url = {http://smartech.gatech.edu/handle/1853/26936}, author = {Antonio Rey and Andrzej Koli{\'n}ski and Jeffrey Skolnick and Yehudi K. Levine} }