Welcome to the Bio-molecule Stretching Database
The Biomolecule Stretching Database (BSDB) contains information related to mechanical stretching of biomolecules. Currently, the database is restricted to proteins and to stretching at constant velocity.When plotting the force of resistance to pulling, F, versus the pulling distance, d, one may encounter one or more isolated force peaks on the way to full stretching. the characteristic scale of F is characterized by Fmax - the maximum force in an isolated force peak. If no force peak develops, Fmax is assigned a value of zero. Usually, this happens when some disulphide bonds prevent full stretching.
The Database lists results obtained theoretically within a structure-based coarsegrained model, initially, for 17 134 structures with no more than 250 amino acids as discussed in reference: M. Sikora, J. I. Sułkowska, and M. Cieplak, Mechanical strength of 17 134 model proteins and cysteine slipknots, PLoS Computational Biology, 5 e1000547 (2009). The database is further described in: M. Sikora, J. I. Sulkowska, B. S. Witkowski, and M. Cieplak, BSDB: the biomolecule stretching database, Nucl. Acid Res. 39, D443-D450 (2011).
Multi-domain proteins are discussed in reference: M. Sikora and M. Cieplak. Mechanical stability of multi-domain proteins and novel mechanical clamps, Proteins: Struct. Funct., and Bioinf. 79(6) 2011, where 315 proteins are considered.
In the first two papers, we have used terms "cysteine knot" and "cysteine slipknots" instead of the correct terms "cystine knot" and "cystine slipknot" respectively. Further analysis of the cystine slipknot proteins can be found in reference: L. Peplowski, M. Sikora, W. Nowak, and M. Cieplak, Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations, J. Chem. Phys. 134, 085102 (2011).
It also lists experimental results on Fmax that are available in the literature. Furthermore, it provides information on Fmax as obtained within all-atom simulations. The users are encouraged to submit new theoretical and experimental entries to us and to request calculations for proteins that are not yet stored in BSDB.
The research leading to creation of this database has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement 213382 (FUNMOL)