| |
Some software that might be useful
pathdriven-tclForces.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 data-sets.
|
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 algencan-pocket.f
Used in:
M. R. B. Batista, L. MartÃnez, 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]
|
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. 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]
|
|
|
|
|