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ordancat [2013/10/09 08:22] – created rkissordancat [2014/01/01 15:52] (current) – flack
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 ====== Order analogs from catalogs (hit expansion) ====== ====== Order analogs from catalogs (hit expansion) ======
  
-[[http://youtu.be/T8ZSKDZuEcI|{{:hello.png?100|}}]] **[[http://youtu.be/T8ZSKDZuEcI|Check out how Ed, the chemist finds analogs for his hit using Mcule >>]]**+[[http://youtu.be/T8ZSKDZuEcI|{{:hello.png?100|}}]] **[[http://youtu.be/T8ZSKDZuEcI|Check out how Ed, the chemist finds analogs for his hit using Mcule »]]**
  
-**__[[ordancatsingle|Search close analogs for a single hit >>]]__**+**[[ordancatsingle|Search close analogs for a single hit »]]**
  
-**__[[ordancatmulti1search|Search analogs for multiple hits by a single search >>]]__**+**[[ordancatmulti1search|Search analogs for multiple hits by a single search »]]**
  
-**__[[ordancatmultimoresearch|Search analogs for multiple hits (one hit at a time) >>]]__**+**[[ordancatmultimoresearch|Search analogs for multiple hits (one hit at a time) »]]**
  
-**__[[ordancatsinglediv|Search for more diverse analogs of a single hit >>]]__**+**[[ordancatsinglediv|Search for more diverse analogs of a single hit »]]**
  
-== A) Search close analogs for a single hit ==+--
  
-If you have a single hit and want to search and order its close analogs, follow these steps:  +**[[usecases|Go back to use cases »]]**
- +
-1. Go to **[[http://mcule.com/search|"FIND CHEMICALS / SINGLE QUERY"]]** +
- +
-2. Specify your query (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) +
- +
-3. If you want to keep a particular substructure in all resulting analogs, modify your query accordingly (delete unnecessary parts) and select **"Substructure"** search type. Note: you can block substituents at particular positions of the molecule by placing explicit hydrogen atoms. +
- +
-4. If you simply want the overall most similar analogs of your compound, select **"Similarity"** search type +
- +
-5. Click on **"SEARCH"** +
- +
-6. After the search was finished and the most similar compounds were displayed, click on the orange **"QUOTE"** button in the top right corner +
- +
-7. Fill out the quote form +
- +
-8. Click on either **"INSTANT QUOTE"** (quote will be generated on-the-fly - **[[https://mcule.com/pricing|subscription required]]**) or **"NEXT-DAY QUOTE"** (we will send you a quote by e-mail in 24-48 hours) +
- +
-**__[[usecases|Go back to use cases >>]]__** +
- +
-== B) Search analogs for multiple hits by a single search == +
- +
-If you have multiple hits containing common structural elements (e.g. multiple analogs of the same scaffold), it make sense to include all your hits in a single search as multiple queries. +
- +
-1. Go to **[[http://mcule.com/???|"FIND CHEMICALS / MULTIPLE QUERY SIMILARITY"]]** +
- +
-2. Specify your queries in SMILES, mcule ID, InChI or SDF formats (use the tabs on the left to **"Paste text"** or **"Upload file"**) +
- +
-3. You can set the similarity **"Scoring method"** under **"Advanced options"**: **//Best//** scoring method will pick the similarity score to the most similar query molecule. **//Average//** scoring method will calculate an average similarity score to all query molecules. +
- +
-4. Under **"Advanced options"** you can also set the **"Descriptor"** used for the similarity search (**OpenBabel Linear Fingerprint**, **OpenBabel MACCS Keys**, **Indigo Similarity Fingerprint**) +
- +
-5. Click on **"SEARCH"** +
- +
-6. After the search was finished and the most similar compounds were displayed, click on the orange **"QUOTE"** button in the top right corner +
- +
-7. Fill out the quote form +
- +
-8. Click on either **"INSTANT QUOTE"** (quote will be generated on-the-fly - **[[https://mcule.com/pricing|subscription required]]**) or **"NEXT-DAY QUOTE"** (we will send you a quote by e-mail in 24-48 hours) +
- +
-**__[[usecases|Go back to use cases >>]]__** +
- +
-== C) Search analogs for multiple hits (one hit at a time) == +
- +
-If your hits are from fairly different scaffolds, it might make more sense to run separate similarity searches on each of them, merge the results into a single compound collection, and request a quote for the merged collection. +
- +
-1. Go to **[[http://mcule.com/search|"FIND CHEMICALS / SINGLE QUERY"]]** +
- +
-2. Specify your first query (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) +
- +
-3. If you want to keep a particular substructure in all resulting analogs, modify your query accordingly (delete unnecessary parts) and select **"Substructure"** search type. Note: you can block substituents at particular positions of the molecule by placing explicit hydrogen atoms. +
- +
-4. If you simply want the overall most similar analogs of your compound, select **"Similarity"** search type +
- +
-5. Click on **"SEARCH"** +
- +
-6. Repeat steps 1-5 for all your hits +
- +
-7. Go to **[[http://mcule.com/collection|"COLLECTIONS"]]** +
- +
-8. You can select your most recent collections (results of your analog searches) and click on **"MERGE"** to merge them into a single collection +
- +
-9. Alternatively, you can open your most recent collections one by one, select the most interesting compounds and click on the **"ADD TO"** button to add them to a new or an already existing collection +
- +
-10. Go to the final collection that contains the selected analogs you would like to order and click on the orange **"QUOTE"** button in the top right corner +
- +
-11. Fill out the quote form +
- +
-12. Click on either **"INSTANT QUOTE"** (quote will be generated on-the-fly - **[[https://mcule.com/pricing|subscription required]]**) or **"NEXT-DAY QUOTE"** (we will send you a quote by e-mail in 24-48 hours) +
- +
-**__[[usecases|Go back to use cases >>]]__** +
- +
-== D) Search for more diverse analogs of a single hit == +
- +
-If you are looking for compounds with similar pharmacophore properties but more structural diversity you can use **[[http://mcule.com/apps/1-click-scaffold-hop|1-Click Scaffold Hop]]** to find new interesting scaffolds. +
- +
-1. Go to **[[http://mcule.com/apps/1-click-scaffold-hop|"LEAD OPTIMIZATION / 1-CLICK SCAFFOLD HOP"]]** +
- +
-2. Depending on your **[[http://mcule.com/pricing|Price plan]]**, you can choose from input collections with different sizes +
- +
-3. Specify your query (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) +
- +
-4. Click on **"SCAFFOLD HOP"** +
- +
-5. After the results are displayed you can visualize the similarity between the query and each identified analog by clicking on the **"VISUALIZE SIMILARITY"** button +
- +
-6. To request a quote for any particular analog, you can click on the orange **"QUOTE"** buttons. Alternatively, you can click on the MCULE ID of a particular analog to display its index page, where you can click on **"ADD TO"** to add the analog to a new or an already existing compound collection. Then go to **[[http://mcule.com/collection|"COLLECTIONS"]]**, open the collection containing the selected analogs and click on the orange **"QUOTE"** button in the top right corner. +
- +
-7. Fill out the quote form +
- +
-8. Click on either **"INSTANT QUOTE"** (quote will be generated on-the-fly - **[[https://mcule.com/pricing|subscription required]])** or **"NEXT-DAY QUOTE"** (we will send you a quote by e-mail in 24-48 hours) +
- +
-**__[[usecases|Go back to use cases >>]]__**+
  
ordancat.1381306938.txt.gz · Last modified: 2013/10/09 08:22 by rkiss