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Below, we have listed ReCore Fragment Indices which are ready for you to use in LeadIT/ReCore. Please mind that you can most certainly create your own Indices. See the manual, or just write to

leadit@biosolveit.de in case you need help. 

A)

The fragment database that is within the download package is based on a subset of the DUD dataset (www.docking.org), which is a subset of the ZINC 'leadlike' set, actives from 40 different targets and molecules similar to these actives.

The set has further been filtered to contain only the first appearance of a so-called Murcko-Scaffold in a compound. A Murcko-Scaffold is defined as: 'Contiguous ring systems plus chains that link two or more rings, as defined in "The Properties of Known Drugs. 1. Molecular Frameworks", Guy W. Bemis and Mark A. Murcko, J. Med. Chem. 1996, 39, 2887-2893.'

This ReCore Fragment Index is a small, 'to play with'-set with which customers can test out all the functionality of ReCore to get going.

B)

A larger ReCore Fragment Index can be downloaded from our website (www.biosolveit.de/LeadIT, then go to the download icon)  which is derived from all molecules that are in the Zinc ’leadlike’ dataset. When ’expanded’ (i.e., when the actual index is created using the accompanying script), this is the largest of all datasets with a size of 6.5GB.

As set A) this index has further been filtered to contain only the first appearance of a so-called Murcko-Scaffold in a compound. A Murcko-Scaffold is defined as: 'Contiguous ring systems plus chains that link two or more rings, as defined in "The Properties of Known Drugs. 1. Molecular Frameworks", Guy W. Bemis and Mark A. Murcko, J. Med. Chem. 1996, 39, 2887-2893.'

If customers want to do serious research they should download this data and extract it overnight.


C)

The CSD-based ReCore Fragment Index has been filtered to not contain metals, salts, but only core organic chemistry of observed 3D small molecule crystal structures. The underlying starting compounds amount to around 100k molecules. This ReCore Fragment Index can be downloaded from the CCDC website only and requires you to be a CCDC/CSD customer.

The procedure we followed here has first been used by Hoffmann-LaRoche and is published in the original ReCore publication by Maass et al.

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All the compilations contain molecules, a batch file to ’expand’ the input files to the actual Fragment Index, an ASCII file with rules for shredding, so-called cut files (fragments in a certain format), and so-called pruned cut files for the ReCore Index File (*.rsx) generation.