Discussion

Sunghwan Kim | Mon, 04/17/2017 - 15:36
Hi, Kyle, Please send me an email at kimsungh at ncbi.nlm.nih.gov, with ccing your course instructor at SUNY Potsdam. Sunghwan,

OLCC S32 | Mon, 04/17/2017 - 14:51
Hello Dr. Kim, I'm taking this class with Dr. Martin Walker at SUNY Potsdam. For the student projects I was looking into this one, I was wondering if there was any information to starting this project? Thank you, Kyle J. Cassidy

Anja Brunner | Fri, 04/14/2017 - 02:49
Hi Nwume, I think that the search in Reaxys that Dr. Ridley describes above is an excellent way to delve into a topic and explore what areas are of most interest to you. He also shows you how to use the filters to narrow down hitsets. If you are specifically interested in Ziprasidone, enter that name into the Quick Search in Reaxys. You will get a Substance Record and over 7000 Document Records. I encourage you to spend some time exploreing the Substance Record to get a feel for the tremendous amount of information it contains. You have identifier information, a link to the Synthesis Planner, and a large body of property information: physical, spectral, bioactivity, uses and more. Each excerpted property entry is connected to the citation of the source document so you can always look at the context in which the data were reported. Also explore the Document Records. They are first organized by Relevance but you can use the filters to, for example, look at only Reviews or other document types. I personally like using the Index Term Filter. It quickly gives me an overview of the topics addressed in the full set of documents to (a) get a feel for what topics are most commonly associated with and addressed regarding Ziprazidone and (b) select the documents that address topics that I find interesting. The Index Terms in each Document Record is also a very interesting way of finding other search terms you may not have thought of and that can help narrow or expand your search. Give it a shot and see what you find. Have fun! Anja

Damon Ridley's picture
Damon Ridley | Thu, 04/13/2017 - 17:51
Bob Good question! (And I have often wondered why myself.) I think the answer is 'historical' and traces back to the fact that the default structure search in Reaxys (and its predecessors) is 'As drawn' which mostly means that positions are blocked unless you 'open' then. This is the reverse for many other products where the default structure search is 'by substructure' and then you need to 'close' ("lock") positions where you don't want further substitution. When you want to 'open' a position in Reaxys you can 'open' up to various extents and the node then is shown annotated (s#) where # can be 1,2,3 etc to indicate the number of further substituents allowed. The annotation used to 'fully open' is: (s6). Personally, I don't use this to open a specific node in MarvinJS. Instead, I right click on the node, go to the Advanced Tab and then adjust the Substitution box to what I want. Note that if you want to allow all substitutions or just substitutions on heteroatoms then MarvinJS has a box at the top right of the Structure Editor to do this. Damon

Damon Ridley's picture
Damon Ridley | Thu, 04/13/2017 - 17:30

Time zones! (Your first post that I answered was before 6:00 my time.) Actually, Reaxys does have "mechanism" as an index term in Reaction Records, but it is in the Subject Studied Field. Query builder => Search properties: subject => Drag Subject Studied to the working space. To see terms in the field, click Lookup icon at the very right of the field and in this case you see 16 terms, one of which is: mechanism. Check the box next to it, then Transfer. (Lookup is a very handy tool to help select terms in any field in Query builder.) If you now Search (Reactions) you get around 75,000 reactions that have been specifically indexed as mechanism. To narrow these, click back to Query builder, click Structure icon at the top of the screen, and then build the structure of your cyclohexene anhydride adduct. Click the arrow icon (bottom of panel on left), then click to the left of your structure and drag towards the structure. You then have drawn an arrow that indicates to Reaxys you want the structure to be a product in a reaction. Click Substructure on the right panel, and then Transfer query. You now have a structure query and Subject Studied: mechanism query. Click: Search (Substances). You will get 38 reactions from around 80 documents. If instead you search reaction: structure of butadienesulfone + maleic anhydride => cyclohexene As drawn you don't get any hits. You can also try other structures if you wish, although if you search a very general structure (such as cyclohexene, substructure, as product - i.e., you have drawn the reaction arrow as above) you will find the search takes several minutes to complete. In such cases you can try Similar rather than Substructure as your search type. All this is possible because you can search text terms in Reaction Records in Reaxys. I hope this helps. Damon

OLCC S197 | Thu, 04/13/2017 - 17:26
hy, to be be specific i am working on finding the properties of ziprasidone which is an anti-psychotic drug using pubchem and reaxys i want to compare the result gotten from the two. from nwume

Robert Belford's picture
Robert Belford | Thu, 04/13/2017 - 15:40
on this tutorial,<a href="http://supportcontent.elsevier.com/RightNow%20Next%20Gen/Reaxys/New_RX_Substance_Searching_Workflow_12-16-2016.pdf">http://supportcontent.elsevier.com/RightNow%20Next%20Gen/Reaxys/New_RX_Substance_Searching_Workflow_12-16-2016.pdf</a> step 8.e has you set the substituents to 6, so the atoms are labeled (s6). What is the value of the number? Why 6? I may discover later, but I am not sure what this parameter does. Thanks, Bob

Olcc S10 | Thu, 04/13/2017 - 13:46
Yes sir. That is what I was thinking. Emily

Robert Belford's picture
Robert Belford | Thu, 04/13/2017 - 13:41
so you are saying, if you have an unknown, and you make measurements, like a boiling point, molar mass, melting point, could you put those into a spreadsheet, and pull out of PubChem all molecules that cover that range? And also, limit it to a defined set of molecules? That is, sort of like an "AND" Boolean functions. [List of Molecules] AND [mp -01:01] AND [bp 99:101] AMD [MS 17:19].... Or just get a list of all molecules with a given boiling point?

Olcc S10 | Thu, 04/13/2017 - 13:06
My idea is if we had a list of 50 unknown chemicals could we get the names from the properties. This would be useful for analytical labs to help them with a lab where they have to identify the chemicals given to them. Emily