Virtual Computational Chemistry Laboratory

Software Groups of Indices Contributor


GSFRAG-L Descriptor block for the VCCLab Project

General information. The GSFRAG-L program is an extension of the program GSFRAG. It allows one to calculate the occurrence numbers of special molecular fragments on k=2,...,7 vertices containing one labeled vertex. Occurrence numbers can be used as molecular descriptors in quantitative structure-property/activity studies in order to describe the effect of hetero atoms.

Description of fragments. Let us consider unlabeled molecular fragments of the same structure as in the GSFRAG program. Each fragment consists of one or more disconnected components (primary fragments): paths of length n, 1?n?6 (denoted by symbol "pn"), cycles on m vertices, 3?m?7 (denoted by "cm"), or paths (cycles) with a number of attached chains of unit length (we label each atom of the path/cycle by the Latin capital A, B, etc. and list labels of atoms corresponding to attached chains after the path/cycle name). A name of the whole fragment is formed by concatenating names of each individual component. In the GSFRAG program such fragments are called "basic". In the next step we mark one of the atoms in the basic fragment by one of the following labels: C, N, O, S, Cl, Br, I, F. So we get a molecular fragment with one labeled vertex. Atoms in the unlabeled fragment are numbered sequentially (in paths/cycles with attached chains atoms of the path/cycle are numbered first). A name of the labeled fragment is formed by adding to the unlabeled fragment name (after a dash) the number of labeled atom and the label name. Examples of molecular fragments with a labeled vertex are given in the picture below.

Applications. Molecular fragments of this type provide good correlations between properties and chemical structure for many classes of compounds. Corresponding molecular descriptors are expected to be widely used in QSAR/QSPR studies.
 

References

  1. Skvortsova M.I., Baskin I.I., Skvortsov L.A., Palyulin V.A., Zefirov N.S., Stankevich I.V. Chemical graphs and their basis invariants. J. Mol. Structure (Theochem). 1999. 466 (1-3) 211-217.
  2. Skvortsova M.I., Fedyaev K.S., Baskin I.I., Palyulin V.A., Zefirov N.S. A New Technique for Coding Chemical Structures Based on Basis Fragments. Doklady Chemistry. 2002. 382 (4-6) 33-36. Translated from: Doklady Akademii Nauk (Russ.), 2002. 382 (5) 645-648.
  3. See FAQ if you have questions. How to cite this applet? Are you looking for a new job in chemoinformatics?

Copyright 2001 -- 2016 http://www.vcclab.org. All rights reserved.