BioPhysConnectoR (version 1.6-5)

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, chains=NULL, eps = 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

eps

tolerance

file

to store the results in file, the file name prefix has to be given

im

interaction matrix, per default each interaction strength equals 1

Value

• Returns a list with the following components
• $q
  fraction of native contacts
• $fe
  free energy
• $ie
  internal energy
• $p
  probability vector
• $iter
  number of iterations
• $b
  vector containing the B factors

Details

If a file name prefix is given, the output is directed to three files. The file ending with _qfi.out covers the following information: "t q fe ie i". The files _p.out and _bfacs.out contain "t" followed by the probabilities or the B factors for each amino acid.

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
res<-scpcp(cm = cm, eps = 10^(-10), t = 5, r = 0.8, maxiter = 100,
           pstart = 0.5, chains=chains)