ROTATE

Does ROTATE identify conformations having close contacts?

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

Can ROTATE cluster the generated conformations?

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.

Does ROTATE use a force field to optimize the geometries?

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.

Does ROTATE perform a systemic and exhaustive search in conformation space?

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

How is ROTATE cited correctly in publications?

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).

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