Self-Consistent Pair Contact Probability Approximation

Description

The model of the Self-Consistent Pair Contact Probability (SCPCP) (Micheletti et al., 2001; Hamacher et al., 2006) computes equilibrium properties of structures with known native states. For a given contact map, extracted from a PDB file or artificially created, the fraction of native contacts, the free and internal energies are computed as well as the degree to which an amino acid is in its native state conformation. The maximum number of iteration and the preferred accuracy for the approximation can be specified.

Usage

scpcp(T, R, cm, pstart = 0.5, maxiter = 2000, chains=NULL, maxtol = 1e-11,
      file = NULL, im = NULL)

Arguments

Details

Results of each iteration as well as the final results are written into the given output file.

Value

Returns a list with the following components

Author(s)

Franziska Hoffgaard

References

Micheletti, Banavar, Maritan (2001) Physical Review Letters 87, 088102-1.
Hamacher, Trylska, McCammon (2006)PLoS Computational Biology 2, e10.
Hamacher (2009) Eur. Biophys. J., in press.

Examples

## Not run: 
p<-extractPDB(system.file("1KZK.pdb", package = "BioPhysConnectoR"))
cm<-build.contacts(n = p$lca, xyz = p$coords, cuts = 169)$cm
chains<-p$chains
im<-build.interact(cseq=p$caseq,d=chains,mj1=matrix(0.05,20,20),alpha=1)
res<-scpcp(cm = cm, maxtol = 10^(-10), T = 5, R = 0.8, im = im, 
	   maxiter = 10, pstart = 0.5, chains=chains)

## End(Not run)

Results