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Conformer search methods


#1

from where can i find algorithms of particular confomer search methods? any papers available for weighted rotor search and random rotor search?


#2

It’s a little old but I think it formed the basis for how all the searching in MacroModel (from Schrödinger) is done.

J. Am. Chem. SOC. 1990, 112, 1419-1427
DOI: 10.1021/ja00160a020


#3

There are not specific papers on these methods (from Open Babel). They are based, in part, on methods used in OpenEye OMEGA:

  • Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and the Cambridge Structural Database J. Chem. Inf. Model. 2010, 50, 572-584. DOI: 10.1021/ci100031x
  • Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures. J. Chem. Inf. Model. 2012 52, 2919–2936. DOI: 10.1021/ci300314k

The rulesets for finding rotatable bonds are similar between Open Babel (and thus Avogadro) and OMEGA.

The random rotor search method simply tries a set of random conformers and will preferentially pick the lowest.

The weighted rotor search method will adjust weights to particular bond rotations as it runs (e.g., if one conformer is low in energy, it will “learn” akin to Monte Carlo).