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search [2013/02/26 17:00]
rkiss [How to use]
search [2013/10/10 18:05] (current)
flack
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 {{:​findchem3.png?​1000|}} {{:​findchem3.png?​1000|}}
  
-Extremely fast and easy-to-use web interface that helps to find purchasable chemicals in the high quality database of mcule.+Extremely fast and easy-to-use web interface that helps to quickly ​find purchasable chemicals in the high quality database of mcule.
  
 ===== When to use ===== ===== When to use =====
  
-[[https://​mcule.com/​search|Find Chemicals]] can be used to find specific compounds/​chemicals or close analogs of a single compound and purchase them by just a few clicks.+[[https://​mcule.com/​search/|Find Chemicals]] can be used to find specific compounds/​chemicals or close analogs of a single compound and purchase them by just a few clicks.
  
 ===== How to use ===== ===== How to use =====
  
-[[https://​mcule.com/​search|Find Chemicals]] has two interfaces: [[https://​mcule.com/​search|Single]] and [[https://​mcule.com/​search/​multi|Multiple]].+[[https://​mcule.com/​search/|Find Chemicals]] has two interfaces: [[https://​mcule.com/​search/|Single]] and [[https://​mcule.com/​search/​multi/|Multiple]].
  
 === Find Chemicals - Single === === Find Chemicals - Single ===
  
-This interface was designed to quickly search the [[purchasable|Purchasable compounds collection]] of the mcule database. +The query molecule can be specified by the [[sketcher|Drawer]] or by entering mcule IDs, [[http://​www.daylight.com/​dayhtml/​doc/​theory/​theory.smiles.html|SMILES]] strings or [[http://​www.inchi-trust.org/​inchi|InChIs]].
- +
-The query molecule can be specified by the [[sketcher|Drawer]] or by entering mcule IDs, SMILES strings or InChIs.+
  
 The following search types are available: The following search types are available:
- 
- 
  
 **[[similaritysearch|Similarity searching]]** can be used to retrieve close analogs of a query molecule (e.g. an [[http://​en.wikipedia.org/​wiki/​High-throughput_screening|HTS]] hit). **[[similaritysearch|Similarity searching]]** can be used to retrieve close analogs of a query molecule (e.g. an [[http://​en.wikipedia.org/​wiki/​High-throughput_screening|HTS]] hit).
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 **[[exactsearch|Exact searching]]** can be used to find a specific compound (e.g. a reference ligand). **[[exactsearch|Exact searching]]** can be used to find a specific compound (e.g. a reference ligand).
  
 +=== Find Chemicals - Multiple ===
 +
 +This interface runs [[exactsearch|exact searches]] with multiple query molecules.
 +
 +It can be very useful for ordering a set of ligands in one step. Virtual screening hit lists with mcule IDs, [[http://​www.inchi-trust.org/​inchi|InChI]] or [[http://​www.daylight.com/​dayhtml/​doc/​theory/​theory.smiles.html|SMILES]] strings and even SDF files can be pasted or uploaded and used as the query of the search.
 +
 +Note that different query types might store different level of information about your query molecules. Searching for mcule IDs is the most straightforward and effective way to retrieve a set of molecules from the mcule database. For example, if you have downloaded the [[purchasable|Purchasable compounds collection]] of the mcule database from [[https://​mcule.com/​database/​|here]],​ and you want to come back for [[delivery|purchasing some compounds]],​ it is suggested that you paste mcule IDs instead of SDF entries here. Note that mcule IDs are always included in exported SDF as a separate SDF field.
  
-Queries can be drawn by the [[sketcher|molecule sketcher]], which can be hidden and reopened by clicking on the “Hide/​Show sketcher” link. Queries can be also defined by entering mcule IDs,  [[http://​www.inchi-trust.org/​inchi|InChI]] or [[http://​www.daylight.com/​dayhtml/​doc/​theory/​theory.smiles.html|SMILES]] strings into the input field. 2D representations can be generated by clicking on the “Generate 2D” button. Note: If the “Generate 2D” button was clicked, the search will be performed on the generated 2D representation (2D SDF exported from the [[sketcher|sketcher]]). If, however, the “Generate 2D” button was not clicked, the search will be directly performed on the mcule ID,  [[http://​www.inchi-trust.org/​inchi|InChI]] or [[http://​www.daylight.com/​dayhtml/​doc/​theory/​theory.smiles.html|SMILES]] strings coming from the input field. The results might be slightly different in these two cases.+===== Results =====
  
-You can select on which [[collmanagement|collection]] the search ​will be performed ​in the “Input collection” field. By default, the [[purchasable|“Purchasable compounds collection”]] is set as input collection. Other collections (e.g. public collections or your previously created collections) can be also selected.+  * Molecules satisfying search criteria 
 +In case of [[similaritysearch|similarity searching]]
 +  * Tanimoto coefficient showing ​the similarity between the query and the target molecules ​will be displayed as a single column ​in Table and List views 
 +  * Hits will be ordered by similarity score
  
-The “Maximum ​hits” field is set to 1,000 by default. If you don't want to limit the number of results, you can delete ​the number from this fieldNote that if you are using the [[freepackage|Free package]], the maximum number of molecules in a single collection is 10,000, which implicitly limits the “Maximum hits” ​to 10,000.+For queries submitted by Find Chemicals Single a maximum of 1000 hits will be displayed. If you would like to get more than 1000 hits, you can use the Workflow Builder with the. Please note however, ​that size of the output collections in the [[freepackage|Free package]] ​are limited ​to 10,000.
search.1361894415.txt.gz · Last modified: 2013/02/26 17:00 by rkiss