Program MEMPROT
.. a program for the data fitting of SEC-SAXS experimental curves of detegent solubilized membrane proteins.
If you use MEMPROT, please cite :
Pérez, J. and Koutsioubas, A., Acta Cryst. (2015) D71, 86-93
The program can be downloaded from the Synchrotron SOLEIL website
If you use MEMPROT, please cite :
Pérez, J. and Koutsioubas, A., Acta Cryst. (2015) D71, 86-93
The program can be downloaded from the Synchrotron SOLEIL website
Program DENFERT
... a program for the ab initio “dummy-atom” structural modeling of Biological Macromolecules including the contribution of their inherent hydration layer.
version 2.1 (July 2019)
Developed by Alexandros Koutsioumpas and Javier Pérez
If you use DENFERT, please cite :
A. Koutsioubas & J. Pérez, Journal of Applied Crystallography (2013) 46, 1884 and
A. Koutsioubas, S. Jaksch & J.Pérez, J. (2016). J. Appl. Cryst. 49, 690
The version 2.1 of the program can be downloaded from the Synchrotron SOLEIL website
or from this link.
User manual download
Brief description
DENFERT is implementing a simulated annealing algorithm similar to DAMMIN program by D. Svergun (Biophys. J. 76, 2879-2886) for the restoration of low-resolution structural info of bio-molecules from SAXS and SANS data. The major advantage of DENFERT is that the hydration layer around bio-molecules is taken into account by introducing a second type of beads (hydration beads) in the model.
In the top figure, we see an example of the shape restoration of Lysozyme from SAXS data using DENFERT. A cartoon representation of the crystallographic structure is also presented for comparison. The bottom figure depicts additionally the hydration layer around the reconstructed protein shape.
version 2.1 (July 2019)
Developed by Alexandros Koutsioumpas and Javier Pérez
If you use DENFERT, please cite :
A. Koutsioubas & J. Pérez, Journal of Applied Crystallography (2013) 46, 1884 and
A. Koutsioubas, S. Jaksch & J.Pérez, J. (2016). J. Appl. Cryst. 49, 690
The version 2.1 of the program can be downloaded from the Synchrotron SOLEIL website
or from this link.
User manual download
Brief description
DENFERT is implementing a simulated annealing algorithm similar to DAMMIN program by D. Svergun (Biophys. J. 76, 2879-2886) for the restoration of low-resolution structural info of bio-molecules from SAXS and SANS data. The major advantage of DENFERT is that the hydration layer around bio-molecules is taken into account by introducing a second type of beads (hydration beads) in the model.
In the top figure, we see an example of the shape restoration of Lysozyme from SAXS data using DENFERT. A cartoon representation of the crystallographic structure is also presented for comparison. The bottom figure depicts additionally the hydration layer around the reconstructed protein shape.