Reaxys Search Strategies
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Various tips and tricks for searching in Reaxys.
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Reaxys Search Strategies
- 1. REAXYS SEARCH STRATEGIES 1 Webinar presented May 21, 2013
- 2. AGENDA • QUERYING METHODS • EFFECTIVE FILTERING • LIST LOGIC • FINDING MARKUSH STRUCTURES 2
- 3. STARTING JUNE 8 ONLY THE NEW UI WILL BE AVAILABLE 3
- 4. FIND PYRROLES 4 Find pyrrole-carboxylic acids (or esters) with a tert- butyl and a phenyl ring anywhere on the structure. There cannot be more than 2 rings. There can be no additional ring closure involving the pyrrole or phenyl ring. Examples: Notice the randomness of the positions of the functional groups.
- 5. FIND PYRROLES: QUERY 5 Retrieves 307 substaances
- 7. LIST LOGIC 7 Are there any isotopes in this list?
- 8. 8 Subtract one list from the other Two isotopic substances are retrieved. 4 3 2 1 6 5
- 9. FIND SPECIFIC ISOTOPES 9 Atorvastatin Find this substance
- 10. 10
- 11. SYNTHESIS OF SPIRO-OXINDOLES: QUERY 11
- 12. 12 How to draw the spiro query structure in MarvinSketch 1 2 5 3 4 6 Use the template, atom, and bond tools to draw the main structure. Select the 5-membered ring tool and attach it to the appropriate atom on the ring. Use the Lasso Select tool to select the bonds on the 5- membered ring Select the Object menu and select Object>Bond>Type>Any Use the Lasso tool to select the atoms in the 5-membered ring. Then click the “More” button, click the “Atom List” button, and then click the “C” and the “N”. Select an atom, right-click, select Edit Atom>Link Node, and then select “L1-2”
- 13. SYNTHESIS OF SPIRO-OXINDOLES: RESULTS 13 Notice that with some reactions the reactant contains the same substructure as the product.
- 15. FILTER AND ANALYZE 15 Analyze the list
- 16. FIND ONE-POT SYNTHESIS OF SPIRO-OXINDOLES: QUERY 16 2 1
- 17. 17 FIND ONE-POT SYNTHESIS OF SPIRO-OXINDOLES: RESULTS
- 18. FIND SUBSTANCES WITH SPECIFIC PROPERTIES: QUERY 18
- 20. 20 FIND SUBSTANCES WITH SPECIFIC PROPERTIES: RESULTS 2 1 3 The hit data is separated from the other data Find specific data by filtering.
- 22. 22 To view the Markush structures in the list, sort by mol wt and then jump to the last page To view the Markush structures for a specific substance, right-click the structure and select “View related markush” Notice that they are from different patents
- 23. VIEWING SUBSTANCES FROM PATENTS 23 How can I view only the real compounds (not Markush)? How can I view just the markush structures and definitions? How can I view those compounds that have pharmacological data and export them to an Excel spreadsheet along with just the pharmacological data? Patent of interest US2012/10235 A1 Search to retrieve a list of substances 2 1 3
- 24. 24 Go to the last page. Select the markush structures and click “Exclude”. Sort by Mol. Wt. 2 1 4 3
- 25. 25 Filter for Bioactivity You may want to exclude some substances before exporting if they are not relevant. For example, these substances contain hundreds of bioactivity data that will take up lots of rows in the Excel sheet. 2 1 3 4
- 26. THANK YOU 26 Contact info: Christine Flemming Product Training Manager c.flemming@elsevier.com Next webinar is: June 6, 2013 1:00 PM EDT The new Reaxys: optimized querying, extended content, and sophisticated result analysis and refinement Training materials are available by clicking the Training link in the Reaxys Help file.
Editor's Notes
- Today I’m going to go through some workflows and show you some querying methods, filtering, and other ways to help you find the answers you need. This is not an intro, so there is an assumption that you have used Reaxys before.
- Just a reminder…….the old Reaxys UI is going away on June 8. At that point only the new UI will be available. But you can move between the 2 UI’s until June 8..
- For today’s session, I have chosen a few scenarios. We would love to get your feedback so that we cover the topics you are interested in for future webinars. A survey will pop at the end so you can share your thoughts.Find Pyrroles- In the first scenario, you want to find pyrroles with certain functional groups anywhere on the substance. Limit it to up to 2 rings and specify no additional ring closure.
- Open the structure editor, draw the fragments, and return to Reaxys. Check the appropriate boxes, as shown. An Rgroup query would bring more specificity to the results but is not required for this search.
- The query retrieves 307 substances. What if you didn’t limit the number of ring closures? All of your results would have at least 2 rings (the query rings) and 1260 substances would be retrieved.What if you didn’t specify “1” fragment? You would retrieve a few more substances, 331 instead of 307.
- Does your list of 307 contain isotopes? In the original query the box for “No isotopes” was not checked, so your list most likely contains isotopes. Re-run the search with the box checked. Then subtract the second list from the first list.
- Use “Create Structure Template from Name” to get the structure for atorvastatin. Bring the structure into the structure editor, draw hydrogens on the phenyl ring, click each hydrogen (one at a time) and select Object>Atom>Isotope>2H. Run the search. Five substances retrieved.
- Instructions for drawing the query are on the next slide.
- 13,159 reactions areretrieved. Notice that with some reactions the reactant contains the same substructureas the product.
- Eliminate reactions where the reactant contains the same substructure as the product. Follow the steps, as shown.
- Try another filter, like “Number of Steps”. Click the Analysis View tool to get an overview of the characteristics of the reactions in the list. You can also filter from the Analysis View tool.
- Use the same query to find “one pot” synthesis reactions. Click the “Reaction Data” button. Type into the “Reaction Basic Index” box.
- To create the query on the preceding slide, click the “Physical” button. If “circular dichroism” and “Optical rotory power” are not on the form, click the “View more fields” link. Type the field name into the box on the left, select the field, and click “Add”. Then click “Save”. Check the boxes in the newly-created form, and click OK. Run the search.
- 32 substances that have any kind of data for circular dichroism and optical rotary power are retrieved. Filter to display only those with a particular optical rotary power (>15).
- Check the box for “Include related Markush”.
- Follow the steps shown, and then run the search.
- To view the Markush substances, sort by Mol. Wt. Then jump to the last page. To exclude them from the list, check the boxes and click the “Exclude” button. To keep only the Markush structures, select them and then click the “Include” button.
- Export the list - Filter this list so that it only contains substances with bioactivity data (keep in mind that the bioactivity data can come from multiple sources, not just the patent that you searched for originally). Now you want to export the list and bio data to an Excel sheet. Before you do this, you might want to scan some of the substances and possibly exclude them before exporting the list. For example, notice that methanol and formaldehyde are in the list and they each contain hundreds of bioactivity data that will take up a lot of rows in your spreadsheet.