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Items tagged with "structure" (11)

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Workflows (9)

Taverna 1 Original Uploader Niall Haslam	GlobPlotExample (v1) Created: 30/04/08 @ 13:14:43 \| Last updated: 30/04/08 @ 14:45:47 Credits: Niall Haslam License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a sample for how to get the new GlobPlot native disorder and globularity prediction webservice working. At the moment it seems you need all the parameters - even the optional ones filled in, to work in taverna. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 0 times Tags (6): disorder \| intrinscially unstructured \| modular protein architecture \| native disorder \| structure \| unfolded	View
Taverna 1 Original Uploader Hamish McWilliam	EBI_MaxSprout (v2) Created: 05/06/08 @ 21:44:00 \| Last updated: 06/06/08 @ 05:58:16 Credits: Hamish McWilliam Attributions: Structure_or_ID License: Creative Commons Attribution 3.0 Unported License Generation of protein backbone and side chain co-ordinates from a C(alpha) trace using the MaxSprout tool. The EBI's WSMaxsprout service (see http://www.ebi.ac.uk/Tools/webservices/services/maxsprout) is used to access the tool. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 62 times \| Downloaded: 40 times Tags (6): backbone \| bioinformatics \| ebi \| pdb \| protein \| structure	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Structure_or_ID (v1) Created: 06/06/08 @ 05:57:31 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format. If a structure identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 379 times \| Downloaded: 37 times Tags (8): bioinformatics \| dbfetch \| ebi \| pdb \| protein \| protein structure \| structure \| structure retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_DaliLite (v1) Created: 07/06/08 @ 17:16:37 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Pairwise structure comparison using the DaliLite tool. The EBI's WSDaliLite web service (see http://www.ebi.ac.uk/Tools/webservices/services/dalilite) is used to access the tool. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 49 times Tags (7): bioinformatics \| ebi \| pairwise structure comparison \| pdb \| protein \| protein structure \| structure	View Download (v1)
Taverna 1 Original Uploader Steffen Möller	Retrieve Single Molecule from ZINC - structure and figure (v1) Created: 24/08/08 @ 22:52:25 \| Last updated: 25/08/08 @ 21:57:16 Credits: Steffen Möller License: Creative Commons Attribution-Share Alike 3.0 Unported License The ZINC database (http;//zinc.docking.org) is a collection of substances with known structures and some chemical characterisation that are commercially available. It is freely available and a much respected resource for computational screening for functional compounds. With the ZINC ID at hand, the ZINC web site is contacted and from there the URL parsed the refence to the real data. This workflow does not scale for regular docking applications. One would retrieve a collection of data inst... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 125 times \| Downloaded: 60 times Tags (4): bioinformatics \| docking \| ligand \| structure	View Download (v1)
Taverna 2 Original Uploader Mark Wilkinson	DataBiNS with Kegg ID (v3) Created: 09/07/09 @ 21:39:54 \| Last updated: 22/11/10 @ 23:16:42 Credits: Mark Wilkinson Fong Chun Chan License: Creative Commons Attribution-Share Alike 3.0 Unported License Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene Rating: 5.0 / 5 (2 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 152 times \| Downloaded: 107 times Tags (8): information \| nssnp \| nucleotide \| OMIM \| pathway \| snp \| structure \| workflow	View Download (v3)
Taverna 2 Original Uploader Kalai	Scoring small molecules for metabolite likeness/ Natural product likeness (v2) Created: 13/05/11 @ 17:22:28 \| Last updated: 18/03/12 @ 16:41:39 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1 Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 66 times \| Downloaded: 16 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| structure \| synthetic \| workflow \| workflows	View Download (v2)
Taverna 2 Original Uploader Kalai	Plotting distribution of natural product likeness scores (v1) Created: 13/05/11 @ 17:34:58 \| Last updated: 13/05/11 @ 17:35:08 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file. - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1 Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 13 times Tags (24): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| plot \| re-use \| structure \| synthetic \| taverna2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Download Structures from PubChem given chemical names (v1) Created: 24/05/11 @ 13:13:52 \| Last updated: 24/05/11 @ 14:19:24 Credits: Kalai Michael Gerlich Attributions: Download Entries from PubChem License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned. The pubchem compound_ID is then used to download structures from PubChem. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 19 times Tags (26): bioinformatics \| cheminformatics \| compound \| data \| download file \| esearch \| eutils \| file \| list \| ncbi \| open science \| open source \| pccompound \| split \| string \| structure \| structure retrieval \| synthetic \| taverna 2 \| taverna2 \| url2list \| workflow \| workflows \| wsdl \| xml \| xpath	View Download (v1)

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Kalai

Natural product likeness filter

Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

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Uploader:

M. Kirsh

A Plane Economy of Space Surfaces From the Mathematics of Einstein and Euclid-Revised

Created: 07/08/09 @ 19:38:05 | Last updated: 21/12/09 @ 17:32:25

Credits: M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

A perspective on nature is introduced based on a visit to the Plane Geometry of Euclid and reinterpretation of the theory of relativity. Nature is redifined as a special case of proximity that is different from normally the construed physical proximity presented to perception. The world is considered as a special case in which the Laws of Motion of Newton and Special Relativity of Einstein are hopefuly united into a single frame. The science of genetics is revisited and new theory ...

File type: Adobe PDF

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