The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix.

ABSTRACT:

Background

The accuracy of any 3D-QSAR, Pharmacophore and 3D-similarity based chemometric target fishing models are highly dependent on a reasonable sample of active conformations. Since a number of diverse conformational sampling algorithm exist, which exhaustively generate enough conformers, however model building methods relies on explicit number of common conformers.

Results

In this work, we have attempted to make clustering algorithms, which could find reasonable number of representative conformer ensembles automatically with asymmetric dissimilarity matrix generated from openeye tool kit. RMSD was the important descriptor (variable) of each column of the N × N matrix considered as N variables describing the relationship (network) between the conformer (in a row) and th

SUBMITTER: Kim H 

PROVIDER: S-EPMC5364127 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature