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User: Paul Dobson
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Name: Paul Dobson Joined: Friday 27 July 2007 @ 15:10:03 (GMT) Last seen: Thursday 02 September 2010 @ 23:39:29 (GMT) Email (public): Not specified Website: http://dobsonlab.blogspot.com/ Location: Manchester, United Kingdom |
Paul Dobson has been credited 13 times Paul Dobson has an average rating of: 4.0 / 5 (2 ratings in total) for their items |
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http://twitter.com/porld
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Not specifiedField/Industry: Cheminformatics
Occupation/Role(s): PDRA
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MIB
The University of Manchester
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Created: 27/02/08 @ 16:21:30 | Last updated: 12/01/12 @ 21:12:15
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
A Pipeline Pilot protocol to search ChemSpider by structure (smiles string) to illustrate use of the ChemSpider wsdl
File type: XML Rating: 4.0 / 5 (2 ratings) | Comments: 0 | Viewed: 250 times | Downloaded: 54 times Tags: |
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Created: 02/11/09 @ 16:15:39 | Last updated: 02/11/09 @ 16:15:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of KEGG compounds which are reffered to by their Inchi strings.
File type: Chemistry Plan Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 13 times | Downloaded: 29 times Tags: |
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Created: 27/05/09 @ 14:33:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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File type: XML Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 8 times | Downloaded: 7 times This File has no tags! |
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Created: 10/02/09 @ 10:51:58 | Last updated: 10/02/09 @ 12:48:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The oxl file represents in ONDEX the SBML reconstruction of yeast metabolism produced in the "Jamboree", as described in the following paper.
PMID 18846089
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Nature Biotechnology. 2008 Oct;26(10):1155-60.
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Lieb...
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Created: 03/06/10 @ 11:39:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M5 which ionises molecules at pH 7 prior to matching, restores original structures.
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Created: 03/06/10 @ 11:38:27
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M4 which generates canonical tautomers prior to matching, matches, then restores original structures.
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Created: 03/06/10 @ 11:35:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M3 which strips stereochemical information from molecules, performs exact matching, and restores stereochemistry.
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Created: 03/06/10 @ 11:33:36
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M2 which reads molecules from two sources and produces clusters of highly similar molecules.
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Created: 03/06/10 @ 11:32:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M1 which matches fully specified molecules on the basis of their canonical representations.
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Created: 20/01/09 @ 10:11:25
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The Wash and Filter workflow performs some processing on incoming structures to filter out those wildcards or unspecified atom types, standardise stereo and charges, and various other adjustments.
This is an advance on the filter used in the paper...
Drug Discovery Today
Volume 14, Issues 1-2, January 2009, Pages 31-40
‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries
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Created: 26/02/09 @ 16:31:21
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow reads a library from an SD file (change the default value of Read_MDL_SD_File) and identifies those structures that conform to Lipinski's Rule of Five.
It then performs a substructure query, represented as SMILES (change the default value on Parse_SMILES), on the structures that pass Lipinski, and creates PNG images of those structures that contain the substructure.
The image results will be found in your Taverna Data folder.
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Created: 03/06/10 @ 11:26:48 | Last updated: 03/06/10 @ 11:30:10
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithms M1-M5 in one workflow, yielding a sparse matrix of matches annotated by match types.
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