Expert's
Corner
Index | Conformation | Position | Divers | Descriptors | Substituents | Regression | Mine | Xray | Peptides | Docking | Fragments | Template | Ab ovo Moloc
Home
Fragment Libraries

Fragment Libraries

General remarks

Fragments (templates) are used in Moloc for Template Maching or Ab Ovo Building. They consist of structures equiped with with extensions, which are 'substituent-points' indicating an atom of attachment and a direction in which an eventual attachment would take place. In Moloc extensions are simply atoms which carry a single-letter label that cannot be mistaken for an atom symbol, followed by a number (e.g. L2). The atom representing the extension will be kept 'as is' in case the extension has not been used in the building process.
A symmetric bond-matrix with rows and columns labeled with the extension labels indicates which extensions can be paired up in the building process. The matrix elements may be zero (no bond allowed), one for single bonds, etc.
Extension labels and bond matrix are defined in a file. Moloc looks for file names starting with 'LABEL'. A default- and exemple file, called LABEL_moloc, can be found in Moloc's 'dat' directory. It is appropriate for templates generated with default parameters.
'Template Matching' typically uses one or a few libraries.
'Ab Ovo Building' has typically several libraries. They contain fragments characterized by various properties: size, rings, aromaticity, etc. In addition, libraries carry three parameters, minimum- and maximum number of fragments to be built into the nascent structure from the library, as well as a frequency parameter, indicating how often it is considered compared to the other libraries (default values: 0, 31, 1). These tokens can help to direct the course of structure building along desired lines.
Furthermore, seed-libraries may be defined, a fragment of which is selected to start the building process. The coordinates of this fragment are either held fixed or are constrained to their initial values.
Library parameters can either be modified interactively (Dyn/o/l/i) or in a list file (.ils) in which several libraries can be specified for input (see option 'Dyn/o/l/g' and its help text).

Generation of a Fragment (Template) Library

We start from 100 molecules from the test set (tst_100.sd in the moloc/dat directory) and generate templates with at least two and at most 7 atoms and at most one cut-bond. The templates in this library contain as many extensions as were found in the generating structures. In order to produce a one-extension only library, proceed as follows: Further options allow to examine and modify libraries: The default procedure is to chop up structures at cut bonds of single-bond type. Alternatively, one can specify a cut-bond library, option 'c', which defines the bonds (substructures) at which cuts should be made. Activate this mode with slider 'c' of the parameter setting option 'p'. A cut-bond library can be found in Moloc's data directory: moloc/dat/shdr_bnd.mab. This file also contains coment lines on how to specify the cuts.

Building a Seed Library interactively

Links

The following URL's lead to publically available databases from which structures for shreddering into templates can be extracted: