User: Paul Dobson

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

13 Friends

1 Group (admin)

5 Groups (member)

8 Workflows

1 Packs

3 Files

1 Favourite

Paul Dobson has been credited 13 times

Paul Dobson has an average rating of:

4.0 / 5

(2 ratings in total)

for their items

Description/summary not set

Other contact details:

http://twitter.com/porld

Interests:

Not specified

Field/Industry: Cheminformatics

Occupation/Role(s): PDRA

Organisation(s):

MIB
The University of Manchester

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Pipeline Pilot Original Uploader Paul Dobson	M5 Charge Matching (v1) Created: 03/06/10 @ 11:39:28 Credits: Paul Dobson 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 19 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M4 Tautomer Matching (v1) Created: 03/06/10 @ 11:38:27 Credits: Paul Dobson 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 14 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M3 Non-stereo Matching (v1) Created: 03/06/10 @ 11:35:03 Credits: Paul Dobson 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 17 times Tags (6): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M2 Similarity Matching (v1) Created: 03/06/10 @ 11:33:36 Credits: Paul Dobson 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 24 times \| Downloaded: 30 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M1 Exact Matching (v1) Created: 03/06/10 @ 11:32:02 Credits: Paul Dobson 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 19 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	C1 Combined Workflow (v1) Created: 03/06/10 @ 11:26:48 \| Last updated: 03/06/10 @ 11:30:10 Credits: Paul Dobson 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 28 times Tags (6): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| pipeline pilot \| systems biology	View Download (v1)
Taverna 1 Original Uploader Paul Dobson	CDK Example (v1) Created: 26/02/09 @ 16:31:21 Credits: Paul Dobson 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 57 times \| Downloaded: 40 times This Workflow has no tags!	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	Wash and filter molecules (v1) Created: 20/01/09 @ 10:11:25 Credits: Paul Dobson 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 177 times \| Downloaded: 59 times Tags (2): metabolite-likeness \| pipeline pilot	View Download (v1)