Title:
COMPUTER-BASED MODELLING OF LIGAND/RECEPTOR STRUCTURES
Document Type and Number:
WIPO Patent Application WO2002016930
Kind Code:
A3
Abstract:
Method for defining a binding site in biological macromolecule based on two-sphere grid and method for determining the free energy of ligand/RNA structure based on pseudo-energy values. These methods can be use in docking and also in high-throughput in silico screening of ligand libraries against RNA structures. Defining the binding site involves: (a) placing a grid over a 3D representation of the receptor; (b) identifying as an excluded volume grid point(s) which lie within the receptor; (c) centring a large sphere over grid point(s) and removing the grid points within the sphere if it does not overlap with the receptor; (e) centring a small sphere over all remaining grid points and determining whether one or more grid points within the small sphere overlap with the excluded volume of the receptor and identifying any non-overlapping grid points as representing a putative binding site cavity within the receptor.
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Inventors:
AFSHAR MOHAMMAD MICHEL (GB)
MORLEY STEPHEN DAVID (GB)
MORLEY STEPHEN DAVID (GB)
Application Number:
PCT/GB2001/003743
Publication Date:
January 16, 2003
Filing Date:
August 21, 2001
Export Citation:
Assignee:
RIBOTARGETS LTD (GB)
AFSHAR MOHAMMAD MICHEL (GB)
MORLEY STEPHEN DAVID (GB)
AFSHAR MOHAMMAD MICHEL (GB)
MORLEY STEPHEN DAVID (GB)
International Classes:
G16B15/30; G01N33/566; C07B61/00; (IPC1-7): G06F19/00; G01N33/68
Domestic Patent References:
| WO1999058722A1 | 1999-11-18 |
Other References:
FILIKOV ANTON V ET AL: "Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.", JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 14, no. 6, August 2000 (2000-08-01), pages 593 - 610, XP008004783, ISSN: 0920-654X
BOEHM HANS-JOACHIM: "Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs.", JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 12, no. 4, July 1998 (1998-07-01), pages 309 - 323, XP008004781, ISSN: 0920-654X
RAREY MATTHIAS ET AL: "A fast flexible docking method using an incremental construction algorithm.", JOURNAL OF MOLECULAR BIOLOGY, vol. 261, no. 3, 1996, pages 470 - 489, XP002203342, ISSN: 0022-2836
LIND KENNETH E ET AL: "Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA.", CHEMISTRY & BIOLOGY (LONDON), vol. 9, no. 2, February 2002 (2002-02-01), February, 2002, pages 185 - 193, XP002203343, ISSN: 1074-5521
BOEHM HANS-JOACHIM: "Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs.", JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 12, no. 4, July 1998 (1998-07-01), pages 309 - 323, XP008004781, ISSN: 0920-654X
RAREY MATTHIAS ET AL: "A fast flexible docking method using an incremental construction algorithm.", JOURNAL OF MOLECULAR BIOLOGY, vol. 261, no. 3, 1996, pages 470 - 489, XP002203342, ISSN: 0022-2836
LIND KENNETH E ET AL: "Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA.", CHEMISTRY & BIOLOGY (LONDON), vol. 9, no. 2, February 2002 (2002-02-01), February, 2002, pages 185 - 193, XP002203343, ISSN: 1074-5521
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