Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains.

Journal Article (Journal Article)

The estimation of contact probabilities (CP) from conformations of simulated bead-chain polymer models is a key step in methods that aim to elucidate the spatial organization of chromatin from analysis of experimentally determined contacts between different genomic loci. Although CPs can be estimated simply by counting contacts between beads in a sample of simulated chain conformations, reliable estimation of small CPs through this approach requires a large number of conformations, which can be computationally expensive to obtain. Here we describe an alternative computational method for estimating relatively small CPs without requiring large samples of chain conformations. In particular, we estimate the CPs from functional approximations to the cumulative distribution function (cdf) of the inter-bead distance for each pair of beads. These cdf approximations are obtained by fitting the extended generalized lambda distribution (EGLD) to inter-bead distances determined from a sample of chain conformations, which are in turn generated by Monte Carlo simulations. We find that CPs estimated from fitted EGLD cdfs are significantly more accurate than CPs estimated using contact counts from samples of limited size, and are more precise with all sample sizes, permitting as much as a tenfold reduction in conformation sample size for chains of 200 beads and samples smaller than 10(5) conformations. This method of CP estimation thus has potential to accelerate computational efforts to elucidate the spatial organization of chromatin.

Full Text

Duke Authors

Cited Authors

  • Meluzzi, D; Arya, G

Published Date

  • February 2015

Published In

Volume / Issue

  • 27 / 6

Start / End Page

  • 064120 -

PubMed ID

  • 25563926

Electronic International Standard Serial Number (EISSN)

  • 1361-648X

International Standard Serial Number (ISSN)

  • 0953-8984

Digital Object Identifier (DOI)

  • 10.1088/0953-8984/27/6/064120


  • eng