
Some software that might be useful
pathdriventclForces.tcl
[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. MartÃnez, 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]

covariance.f90
[Download] 
Computes the covariance between two vectors, as function of "time",
that is, as a function of the shift between the two datasets.

modfrac.f90
[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 algencanpocket.f
Used in:
M. R. B. Batista, L. MartÃnez, Dynamics of Nuclear Receptor
Helix12 switch of transcription activation by modeling timeresolved
fluorescence anisotropy decays. Biophys. J. 105(7), 16701680, 2013.
[PDF]

cylinder.f
[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. DuclertSavatier, 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]




