@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} }