Institute of Chemistry - University of Campinas


Some software that might be useful


[Download] - Read the comments on the script to use it.

Applies a generalized SMD force, with variable directions and to multiple atoms. The basic strategy is described in:

Used in: L. Martínez, I. Polikarpov, M. S. Skaf, Only Subtle Protein Conformational Adaptations Are Required for Ligand Binding to Thyroid Hormone Receptors: Simulations Using a Novel Multipoint Steered Molecular Dynamics Approach, J. Phys. Chem. B, 112, 10741, 2008. [PDF]


[Download] - Computes the covariance between two vectors, as function of "time", that is, as a function of the shift between the two data-sets.


[Download] - Will obtain the coefficients of the linear combination of the data in model data files that best fit the experimental.dat data. The coefficients will be between 0 and 1 and their sum will be 1. (if such a solution is possible), and therefore might be interpreted as the fraction of each model contributing to the experimental result.
Compile with gfortran -o modfrac modfrac.f90 algencan-pocket.f

Used in: M. R. B. Batista, L. Martínez, Dynamics of Nuclear Receptor Helix-12 switch of transcription activation by modeling time-resolved fluorescence anisotropy decays. Biophys. J. 105(7), 1670-1680, 2013. [PDF]


[Download] - Computes the maximum cylinder that fits inside a cavity. Read code commentaries to obtain further usage information.

Used in this article, please cite it if the software was useful:
N. Duclert-Savatier, L. Martinez, M. Nilges, T. E. Malliavin, The redudancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations. BMC Structural Biology, 2011, 11:46 [Full Text]
See also:
Author's software page
The TANGO project