NDLI: GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

Content Provider	Springer Nature Link
Author	Richmond, Nicola J. Abrams, Charlene A. Wolohan, Philippa R. N. Abrahamian, Edmond Willett, Peter Clark, Robert D.
Copyright Year	2006
Abstract	Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199–209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.
Starting Page	567
Ending Page	587
Page Count	21
File Format	PDF
ISSN	0920654X
Journal	Journal of Computer-Aided Molecular Design
Volume Number	20
Issue Number	9
e-ISSN	15734951
Language	English
Publisher	Kluwer Academic Publishers
Publisher Date	2006-10-19
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	GALAHAD Hypermolecule Hyperstructure Molecular alignment Pharmacophore Pharmacostere Shape similarity Animal Anatomy / Morphology / Histology Computer Applications in Chemistry Physical Chemistry
Content Type	Text
Resource Type	Article
Subject	Drug Discovery Physical and Theoretical Chemistry Computer Science Applications

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A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches

Using a staged multi-objective optimization approach to find selective pharmacophore models

Incorporating partial matches within multiobjective pharmacophore identification

Ligand-based virtual screening under partial shape constraints

Avalanche for shape and feature-based virtual screening with 3D alignment

Efficient overlay of small organic molecules using 3D pharmacophores

Open3DALIGN: an open-source software aimed at unsupervised ligand alignment

FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules

Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

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Using a staged multi-objective optimization approach to find selective pharmacophore models

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Avalanche for shape and feature-based virtual screening with 3D alignment

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GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D