Differences

This shows you the differences between two versions of the page.

--- search [2013/02/26 15:55] – rkiss
+++ search [2013/10/10 16:05] (current) – flack
@@ Line 5: / Line 5: @@
 {{: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 =====
-[[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 =====
-[[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 ===
-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]]** 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.
+**[[substructuresearch|Substructure searching]]** can be used to find all molecules that contain a specific substructure (e.g. the main scaffold of a reference ligand).
-**[[substructuresearch|Substructure]]** 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).
-**[[exactsearch|Exact]]** can be useful when looking for a specific molecule (e.g. a reference ligand).
+=== Find Chemicals - Multiple ===
+This interface runs [[exactsearch|exact searches]] with multiple query molecules.
-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.
+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.
-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.
+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.
-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 field. Note 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.
+===== Results =====
+  * 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
+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.