MolAlign: an algorithm for aligning multiple small molecules

In small molecule drug discovery projects, the receptor structure is not always available. In such cases it is enormously useful to be able to align known ligands in the way they bind in the receptor. Here we shall present an algorithm for the alignment of multiple small molecule ligands. This algor...

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Bibliographic Details
Published in:Journal of computer-aided molecular design 2017-06, Vol.31 (6), p.523-546
Main Author: Chan, Shek Ling
Format: Article
Language:English
Subjects:
Algorithms
Alignment
Animal Anatomy
Assemblies
Chemistry
Chemistry and Materials Science
Computer Applications in Chemistry
Construction
Documents
Histology
Ligands
Models, Molecular
Molecular Conformation
Molecular Structure
Morphology
Physical Chemistry
Small Molecule Libraries - chemistry
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Summary:In small molecule drug discovery projects, the receptor structure is not always available. In such cases it is enormously useful to be able to align known ligands in the way they bind in the receptor. Here we shall present an algorithm for the alignment of multiple small molecule ligands. This algorithm takes pre-generated conformers as input, and proposes aligned assemblies of the ligands. The algorithm consists of two stages: the first stage is to perform alignments for each pair of ligands, the second stage makes use of the results from the first stage to build up multiple ligand alignment assemblies using a novel iterative procedure. The scoring functions are improved versions of the one mentioned in our previous work. We have compared our results with some recent publications. While an exact comparison is impossible, it is clear that our algorithm is fast and produces very competitive results.
ISSN:0920-654X
1573-4951
DOI:10.1007/s10822-017-0023-8