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usecases [2013/10/09 08:31] – rkissusecases [2013/10/11 20:58] – rkiss
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-====== Typical use cases of Mcule ======+====== TYPICAL USE CASES OF MCULE ======
  
-**__[[ordsingle|Ordering a single compounds >>]]__** +  - **[[usecasehitident|IDENTIFY NEW HITS FOR YOUR TARGET >>]]** 
- +  - **[[opthitlead|OPTIMIZE HITS AND LEADS >>]]** 
-**__[[ordmculelist|Ordering a list of compounds from mcule ID list >>]]__** +  - **[[ordsingle|ORDER A SINGLE COMPOUND >>]]** 
- +  - **[[ordmculelist|ORDER A LIST OF COMPOUNDS FROM MCULE ID LIST >>]]** 
-**__[[ordlist|Ordering a list of compounds >>]]__** +  - **[[ordlist|ORDER A LIST OF COMPOUNDS >>]]** 
- +  - **[[ordancat|ORDER ANALOGS FROM CATALOGS (HIT EXPANSION) >>]]** 
-**__[[ordancat|Order analogs from catalogs (hit expansion) >>]]__** +  - **[[usecasedownload|DOWNLOAD THE MCULE DATABASE AND COME BACK FOR ORDERING >>]]** 
- +  - **[[usecaseprefilter|PREFILTER THE MCULE DATABASE (DESIGN A SCREENING LIBRARY) >>]]** 
-**__[[usecasedownload|Download the Mcule database and come back for ordering >>]]__** +  - **[[usecasedownloadsubset|DOWNLOAD A SUBSET OF THE MCULE DATABASE >>]]** 
- +  - **[[inhouseext|EXTEND YOUR IN-HOUSE COMPOUND DECK >>]]**
-**__[[usecaseprefilter|Prefilter the Mcule database (design a screening library) >>]]__** +
- +
-**__[[usecasedownloadsubset|Download a subset of the Mcule database >>]]__** +
- +
-**__[[inhouseext|Extend your in-house compound deck >>]]__** +
- +
-**__[[opthitlead|Optimize hits and leads >>]]__** +
- +
-==== Hit identification ==== +
- +
-[[http://youtu.be/RCLQFoZj0C4|{{:hello.png?100|}}]] **[[http://youtu.be/RCLQFoZj0C4|Check out how Ed, the chemist identifies new chemical starting points for his project using Mcule >>]]** +
- +
-You can identify new inhibitors/modulators of your target (receptor, enzyme, nucleid acid, etc.) by searching the Mcule database. In Mcule, you can easily build **[[http://en.wikipedia.org/wiki/Virtual_screening|virtual screening]]** workflows by putting together molecular modeling tools like LEGO bricks. Virtual screening workflows are a set of filters and calculations. Filters can eliminate compounds that unlikely binds your target or have other unwanted properties and calculations can rank order the best candidates for example by their estimated binding affinity. You can filter the whole mcule database (over 5 million compounds) with several tools until you select the most promising compounds (10-1000). Additionally, you can order the best hits by just a few clicks. +
- +
-== A) Structure-based virtual screen == +
- +
-Structure-based virtual screening utilizes the 3D structure of the target when searching for new hits. During the screening, predicted 3D structures of small molecules are fitted into the binding site of the experimentally determined or modeled 3D structure of the target (docking calculation). The 3D structures of thousands of large macromolecules have been already determined by X-ray crystallography or NMR spectroscopy and can be easily selected or uploaded in Mcule. Small molecules predicted to form critical interactions with the target get better (more negative) docking scores and are ranked higher. +
- +
-1. Go to **[[https://mcule.com/search/screen/?template=structure-based-virtual-screening|HIT IDENTIFICATION / STRUCTURE-BASED VIRTUAL SCREEN]]** +
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-2. Select the input collection if other than all **[[purchasable|Purchasable compounds]]** of the Mcule database +
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-3. The loaded template workflow includes a number of individual workflow steps that will be executed sequentially on the input collection. Detailed description of the available workflow steps can be found **[[tools|HERE]]**. +
- +
-4. RUN +
- +
-go back and change pm-s and see the results +
-output collection size +
-sampler +
- +
-**__[[usecases|Go back to use cases >>]]__** +
- +
-== B) Ligand-based virtual screen == +
- +
-Ligand-based virtual screening does not utilize the 3D structure of the target when searching for new hits. Instead, it is based on the structure of a reference ligand (endogenous ligand, known inhibitor, etc.) that binds to a target and/or exhibits some beneficial effect. In ligand-based virtual screening, compounds are typically ranked based on the similarity to the reference ligand (query). +
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-**__[[usecases|Go back to use cases >>]]__**+
usecases.txt · Last modified: 2014/01/01 15:23 by flack