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search [2013/02/26 16:43]
rkiss
search [2013/02/27 08:52]
rkiss
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 **[[http://youtu.be/nrTF1Axoztc|WATCH TUTORIAL VIDEO!]]** **[[http://youtu.be/nrTF1Axoztc|WATCH TUTORIAL VIDEO!]]**
  
-{{:findchem2.png?1200|}}+{{: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 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.
  
-was primarily designed for fast searching of the [[purchasable|Purchasable compounds collection]] of the mcule database.  You can use it to run similarity, substructure and exact searches with a single or multiple queries. The query molecules can be specified by ChemWriter (instant appearance, comprehensive set of functionalities) or by entering mcule IDs, SMILES strings or InChIs. Start browsing the results immediately and buy the best hit(s) by just a few clicks.+===== How to use =====
  
-Looking for a single compound, a list of compounds or some close analogs of a compound? This is exactly what Find Chemicals has been designed for.+[[https://mcule.com/search|Find Chemicals]] has two interfaces: [[https://mcule.com/search|Single]] and [[https://mcule.com/search/multi|Multiple]].
  
-===== How to use =====+=== Find Chemicals - Single ==
 + 
 +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 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). 
 + 
 +**[[substructuresearch|Substructure searching]]** can be used to find all molecules that contain a specific substructure (e.g. the main scaffold of a reference ligand). 
 + 
 +**[[exactsearch|Exact searching]]** can be used to find a specific compound (e.g. a reference ligand).
  
-Under the “find chemicals” tab three simple search types are available: **[[exactsearch|“Exact”]]**, **[[similaritysearch|“Similarity”]]** and **[[substructuresearch|“Substructure”]]** searches.+=== Find Chemicals - Multiple ===
  
-**[[exactsearch|“Exact search”]]** can be useful when looking for a specific molecule (e.g. a reference ligand).+This interface runs [[exactsearch|exact searches]] with multiple query molecules.
  
-**[[similaritysearch|“Similarity search”]]** can retrieve close analogs of a query molecule (e.g. an [[http://en.wikipedia.org/wiki/High-throughput_screening|HTS]] hit). “Similarity threshold” ([[http://en.wikipedia.org/wiki/Jaccard_index|Tanimoto coefficient]]) controls how similar the hits from the query need to be.+It can be very useful for ordering a set of ligands in one stepVirtual 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.
  
-**[[substructuresearch|“Substructure search”]]** can be used to find all molecules that contain a specific substructure (e.g. the main scaffold of a reference ligand).+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 [[http://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 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.txt · Last modified: 2013/10/10 18:05 by flack