Paper Citing NAMD - Abstract
Silva, Candida G.; Ostropytskyy, Vitaliy; Loureiro-Ferreira, Nuno; Berrar, Daniel; Dubitzky, Werner; Brito, Rui M. M.
P-found: The protein folding and unfolding simulation repository
PROCEEDINGS OF THE 2006 IEEE SYMPOSIUM ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 101-108, 2006
One of the central challenges in structural molecular biology today is the protein folding problem, i.e. the acquisition of the 3D structure of a protein from its linear sequence of amino-acids. Different computational approaches to study protein folding and protein unfolding have recently become common tools available to the researcher. However, due to the lack of appropriate infrastructures, it is very difficult to directly compare simulations performed by different groups, with different methods, in different experimental conditions or for different proteins. Thus, we set out to create a public data repository with the goal of addressing the problem of comparison, analysis and sharing of information and data on protein folding and protein unfolding simulations. The P-found system for protein folding and protein unfolding simulations is presented. At the moment, the data repository allows uploading of molecular dynamics (MD) protein folding and unfolding simulations, calculates and stores several time series with the variation over time of pre-defined molecular properties, and allows searching and downloading of these data. In the near future, simulations performed by other than MD methods may be uploaded, and data mining techniques for analysis and comparison of multiple simulations will be implemented. The home page for the P-found system is accessible at http://www.p-found.org.
