Local electron affinity mapped onto the isodensity surface of a caprolactam derivative inhibitor
Local electron affinity mapped onto the isodensity surface of a caprolactam derivative inhibitor

ParaFrag is a method for atom-independent bioisoster searching of molecular fragments. The approach is based on similarity comparison of local surface property extrema calculated on isodensity surfaces by semi-empirical molecular orbital methods. The method has been applied for applications in drug design (scaffold hopping). Please see here for additional information.

ParaFrag has been developed together with Timothy Clark (Computer Chemistry Center, Erlangen) and Harald Mauser (F.Hoffmann-La Roche, Basel).

ParaFrag is distributed as part of the ParaSurfTM package by Cepos InSilico. It requires a semi-empiricial molecular orbital program such as VAMP, EMPIRETM or Mopac6.

If ParaFrag is useful for your research please cite the original reference.

Jakobi et al., J Mol Model 14:547-558 (2008) doi: 10.1007/s00894-008-0302-3

Availability

A restricted version of ParaSurfTM and EMPIRETM is freely available for bona fide academic users. Please apply here.