Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this project, we combine three computationally inexpensive simulation methods, (i) normal mode analysis using the elastic network model, (ii) rigidity analysis using the pebble game algorithm, and (iii) geometric simulation of protein motion, to explore conformational change along normal mode eigenvectors.
If you use the results of this calculation in an academic output (such as a patent, a book, a lecture or a paper), please remember to acknowledge our two papers:
- "Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses", E. Jimenez-Roldan, R. Freedman, R. A. Römer, S. A. Wells, Physical Biology 9, 016008-12 (2012), http://dx.doi.org/doi:10.1088/1478-3975/9/1/016008
- "The dynamics and flexibility of protein disulphide-isomerase (PDI): predictions of experimentally-observed domain motions", R. A. Römer, S. A. Wells, J. E. Jimenez-Roldan, M. Bhattacharyya, S. Vishweshwara and R. B. Freedman, Proteins: Structure, Function and Bioinformatics 84, 1776-1785 (2016), http://dx.doi.org/10.1002/prot.25159
This service uses low priority compute cycles at the Scientific Computing Research Technology Platform of the University of Warwick. The service is provided for free at the moment based on a low volume of such requests.
If you wish to use the service more often, please get in touch at @pdb2movie.