Frequently Asked Questions - ROTATE

ROTATE checks all conformations for non-bonded interactions and removes those having close contacts (or atom bumps) automatically.

ROTATE can combine similar conformations into classes and represent each class by a single conformation (class representative). Two different and adjustable similarity criteria can be chosen. One crierion works in Cartesian space, i.e., is based on the RMS(XYZ) (root mean square) deviation of the Cartesian coordinates of all non-hydrogen atoms of the conformations. The second criterion uses the torsion angle space to calculate whether two conformations are similar or not, i.e., the comparison is based on the RMS(TA) deviation of the torsion angles along the rotated bonds of two conformerations.
For both methods, the RMS threshold that is used to define two conformations as similar, can be chosen by the user and both methods provide a balanced sampling of the conformational space.

ROTATE does not use a classical force field algorithm for optimization, but applies a symbolic (or empirical) energy function. This symbolic energy function is derived from the torsion angle library (TAL) that contains the
distribution of torsion angles of over 1,000 four-atomic torsion angle patterns.
The distributions are stored in histogram (from 0 to 360 degree). The frequencies of the individual torsion angle values are used to derive a symbolic energy value for each torsion angle value for a specific torsion angle pattern and a gradient optimizer identifies the minimas.

ROTATE uses a knowledge base of preferred torsion angles of acyclic, rotatable bonds (or rotors). These torsion angles have been derived from a statistical analysis of the conformational preferences of open-chain portions
in small molecule crystal structures xray taken from the CSD system (Cambridge Structural Database) and are stored in the so-called torsion angle library (TAL). Therefore, ROTATE does not perform a "classical" systemic and exhaustive search, but exhaustively searches in this space of allowed torsion angles spanned by the TAL and the generated conformations are biased towards xray geometries.

The best way to cite ROTATE is

(a) Renner, S.; Schwab, C.H.; Schneider, G.; Gasteiger, J.
Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors.
J. Comp. Inf. Model. 2006, 46, 2324-2332.
(http://dx.doi.org/10.1021/ci050075s)
(b) The conformer generator ROTATE is available from Molecular Networks GmbH, Erlangen, Germany (http://www.molecular-networks.com).