BioPhysConnectoR (version 1.6-8)

scpcp: 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

T

temperature

R

distance cutoff between current and native state

cm

contact map

pstart

initial probability value

chains

vector denoting the chain lengths

maxiter

maximum number of iterations

maxtol

tolerance

file

output file name

im

interaction matrix

Value

• Returns a list with the following components
• $free
  free energy
• $intern
  internal energy
• $entropy
  entropy
• $q
  fraction of native contacts
• $bfacs
  vector containing the B factors
• $pi
  probability vector
• $gmat
  resulting G matrix
• $iter
  number of iterations
• $err
  deviation of probabilities

Details

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

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

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)