Today's society uses fossil fuels as an energy source and the carbon dioxide emission is a concern to many scientists. The following youtube video was created by the EPA to describe the consequences of our economic reliance on fossil fuels
Why did the EPA remove this educational information? Are they afraid of science?
It is now defined by a certain cylinder of platinum-iridium alloy, which is kept in France.
This is technically wrong as of May 20, 2019. But in fact, the whole section is wrong, although most people would not notice it, but they no longer define the base units, they define the 7 immutable constants.
Here is what I wrote up in my LT,
must be unlocked with a passwordLate submissions are subject to instructor approval.This assignment is not t
test of hdot in oli
What is the Defense Production Act?
Defense Production Act
White House urges young people to heed COVID-19 warnings
President's message to youth
The following YouTube video does a good job of describing Arrhenius plots.
first video class watched
The publication industry owns science In addition to shaping the content of science, researcher evaluation policies focused on publication statistics contribute to what is essentially a publication industry oligopoly that undermines user access to the research that is published. Because of entrenched journal hierarchies, codified by journal impact factor scores, a handful of large corporate publishers have secure positions in owning “must publish” outlets for scientists. For example, the RELX Group—the corporate owner of the publisher Elsevier, the Scopus database (an aspirational competitor to WoS), the prestigious journals Cell and The Lancet, and the publication database ScienceDirect, among other products—boasts in its 2018 annual report that its Scientific, Technical & Medical division organized “the review, editing and dissemination of 18% of the world’s scientific articles.” By its numbers, the group received a whopping 1.8 million article submissions to 2,500 journals, overseen by 20,000 editors and countless peer-reviewers, and in the process reaped $3.3 billion in revenue. Subscriptions constituted 74% of that revenue. To achieve those revenues, the group continues to expand its offerings: Elsevier published 60% more articles in 2018 than a decade prior.
Is this really the way we want to be?
Just to follow-up on the previous posts, ssmtp is deprecated on Buster, it is no longer maintained. (typical experience with a major system change..., sigh!) The more modern and supported alternative is msmtp.
I installed the code here
Now let’s make an experiment inside the Python shell. Start by typing in the statements shown in the screenshot below
This is very useful and worth checking
Fall 2019 Cheminformatics OLCC
This is a poster worth seeing!!!
education, training, and entrepreneurial/industrial activities in life sciences-related computing.
I think we want to do this landscape, even though she said the opposite.
ow identify and remove those compounds that satisfy all criteria of Lipinski's rule of five.
Doesn't this keep the ones that satisfy the rule of 5, and in step 28 remove the ones that do not? In fact, I do not really understand the "&", . It would seem to me that we would need to loop this through each molecule, But anyways, arn't we removing the ones from the original df that did not follow the rule of 5? (Not removing the ones that do)
Output, one of the of
how do we frame this?
n Python, a distinction between expressi
hlep
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, this material is a modification by Ehren Bucholtz and Robert Belford of CS-POGIL content, with the original material developed by Lisa Olivieri, which is available here.
How can an attribution like this be best preserved in LibreText>
American Journal of M
demo
response.status_code 200
response code in python
Open Parser for Systematic IUPAC Nomenclature
Here we introduce chemical resolvers how OPSIN can help you identify misspelled names, and then as you scroll down, you see an assignment using a spreadsheet that can be obtained from the InChI OER to connect names to PubChem.
The InChI Trust runs an Open Education Resource (OER) w
Here we introduce the InChI OER into LibreText, which can then make the material easy to integrate into any of the interdisciplinary hyperlibraries
sing the InChILayersExplorer show the difference between the InChI for (R)-thalidomide and (S)-thalidomide.
Activity using layers explorer to identify the difference between R and S thalidomide
Lets look at thalidomide, the molecule responsible for the birth defects in figure 2.3.2. Fi
Here we can bring up the ways of representing thalidomide, which we can then use in later examples
Isomers are different molecules with the same atomic constituency,
Introduced stereochemistry with the example of Thalidomide
InChI=1/C2H4ClNO2/c3-1(4)2(5)6/h1H,4H2,(H,5,6)/p+1/t1-/m1/s1
It looks like they forgot the isotope layer
UWPWWENWLZPQGU
The main part of the InChIKey came up with this article in Russian
The K20 mass served as the primary prototype national standard. The other, called K4, served as a “check” standard that monitors the constancy of K20’s mass.
The US actually had two prototypes
interval standard atomic-weight
It might be nice to compare this to the conventional standard atomic weight,
For the 13 elements with standard atomic-weight intervals(hydrogen, lithium, boron, carbon, nitrogen, oxygen, magnesium, silicon, sulfur, chlorine, argon, bromine, and thallium), the standard atomic weight is given as an interval to stress that standard atomic weights are not constants of nature [6]. Each is shown as lower and upper bounds (limits) (Figs. 1.1 and 1.2). Some users of atomic-weight data need a value that is not an interval, such as for purposes of trade and commerce. For these users, a conventional atomic-weight value[4]is
This introduces the concept
he French Revolutionary War, and was originally based on a unit of length, the meter. The earliest definition was the meridional definition, defining the mete
ddd
y Reader's Choice Award fo
temp test
Because both the ST and CT scores range from 0 (for no similarity) to 1 (for identical molecules), the ComboT score may have a value from 0 to 2 (without normalization to unity)
the Combo T has a range of 0 to 2
The clustering threshold may be adjusted by clicking an appropriate position on the similarity score axis (the horizontal line above/below the dendrogram).
This section and the next have dendrograms, that range from 1 (similar) to 0 (dissimilar)
If it is greater than 2 they are substantially different and more electronegative atom completely removes a valence electron from the electropositive,
The rule of thumb is if the difference in electronegativity is greater than 2, the electron is typically removed from the electropositive element and an ion is formed.
Calculate the vapor pressure of water at 45o C if it is 12.79 torr at 15o C, given:
The image on this page was not captured in the web scraping.
eScience is where “IT meets scientists
The four paradigms of science. I believe the slide in figure 1 came from Jim Gray's last talk, which is what this introductory chapter is about.
Session 5.1: Relation between education and society
Abstract: https://www.iupac2019.org/session-5
Would this be a place for IoCT with a focus on Citizen Science? Or would this be a place for Internet in a Box, and the need to provide information to regions that do not have access?
Tools in chemistry education
Abstract: https://www.iupac2019.org/session-5-2
I think this could be a place for the IoCT, and the Virtual Lab.
THEME 4: CHEMISTRY AND SOCIETY
Is this the place for Internet in a Box?
Well, I am thinking twice on this one, as I read through the session abstracts,... https://www.iupac2019.org/chemistry-and-society
mp 3.1: Monitoring Chemicals for a Safer Environment(3 sessions
I think this would be a good place for a talk on IOCT and citizen science, maybe we could bring Stefan in.
On second look, when I say the session abstracts, this may not be the place, https://www.iupac2019.org/symposium-3-1
Symp. 8.2: Digital Chemistry and the Lab of the Future
This is an obvious place for an OER talk, but it would not really be outreach, as these would be people who know about it anyways, and it would be more of a "report", which is not our goal.
This may also be a place for a talk on the Cheminformatics OLCC, especially if we wish to run another this Fall.
education. The role and scope of lab work especially in the first part of tertiary education has undergone quite some changes. The focus and learning goals and outcomes have become better defined. New technology has been introduced in the lab work. Not only analysing tools and tools for recording results have improved. Tools have been developed to assess students in an easier manner. What tools can be used in chemistry education, what is the role of lab work, how can new technology be used in improving chemistry education
terst
perator is a generalization of the concept of a function applied to a function. Whereas a function is a rule for turning one number into another, an operator is a rule for turning one function into another. For the time-independent Schrödinger Equation, the operator of relevance is the Hamiltonian operator (often just called the Hamiltonian) and is the most ub
test of annotation in transcluded page
This chart shows price changes for goods and services from January 1998 to December 2018
note how college textbooks are in on this.
Unfortunately the real spectra have been destroyed in the (conventional) publication process. Even so, these tools can carry our information archeology to make reasonable estimates of what the original spectra might have looked like.
Information archeology
基づく研究手法を
Test to see if hypothes.is works on Japanese (I am really making a link to this cartoon on the fourth paradigm)
Citizen Science
this is a good review article to look for potential participants. We should also look at the next article, "Sensors for Citizens"
ualitative information is based on observables, like ice floats on water, or chlorophyll is green, or the patterns of the lines on your fingerpr
this is great
reparing the Stretch Image for your microSD card
I am assuming we could unzip an image of a particular IIAB and then follow the next step to install it on a micro SD card, and then we could run the Raspberry Pi with it, right?
Jupyter
Jupyter can now be integrated into LibreText
Python Program
This activity is placed in the Thonny editor, but the text strings are red, not green when I use the CKEditor code snippet for python. Does this make sense, and is it an issue?
Presentation: Developing a LibreText and the Application of Hypothes.is Web Annotations to Enhance Student Learning
Presentation on LibreText and Hypothes.is
n experiment to examine the effects of pH on the light absorbing properties of the colored pigments found in red cabbage leaves. The wavelengths of light absorbed bu by the mixture of the
please explain
first demonstrated by Sir Humphry Davy in 1806, and by 1807
Isn't it amazing how creative and determined people can be, to hook up a battery with 3,000 cells! One beauty of LibreText is you can add stuff that you think would interest people to your text.
Click the down-arrow next to Sort by Occurrence and choose Sort by Alphanumerical
When I do this, I get three pages like in figure 3, but there is only one column in each page, not 3. After sorting alphabetically, when I go to the second page, it starts with it starts with further information and ends with mass spectrometry, with the third page starting with solubility.
This has me thinking that the second and third columns are not showing in the overlay.
To help you find relevant citations we offer 'Smart citation suggestions' which use our SmartSearch algorithm to automatically suggest relevant references. To use this feature, place your mouse cursor where you want to insert the citation then click Smart citation suggestions.
Smart Citations are amazing. I am curious if Hdot works on this as it has to be activated.
Gases assimilated with organic solvents become more soluble at higher temperatures.
Can someone provide some additional information on this? I am not seeing it.
Students must have proficiency with technical databases and other resources that enable development of skills in searching the literature, including structure-based searching.
SciFinder and Reaxys covers this
These authors offered a link to a quiz
This is an h. (hypothes.is link to the section of text that links to the MUST test.
Please let me know if it does not open the confchem paper and take you to the part where the link is. ( rebelford@ualr.edu).<br> Thanks
E=q1q2(4πϵ0)
This is a public annotation of some text in LaText, which my students were annotating in the past, and messing up pages.
eithe
I think this needs editing
Substance and Reaction Records, and these enable substances/reactions to be searched precisely in association with words/topics
I understand what is being said here, but is this also why you can combine text and structure search? (I realize that is a different thing, but you had said SciFinder was not set up that way, and so I am wondering)
Requeststhe Director-General to present to it at its 202nd session a plan of UNESCO’s participation in international celebrations of the 150th anniversary of the periodic table of chemical elements in 2019;12.EncouragesMember States to foster the mobilization of extrabudgetary contributions to UNESCO in support of the celebrations of the 150th anniversary of the periodic table of chemical elementsin 2019
Of note
The 150th anniversary of Mendeleev’s periodic table will also take place in 2019 and this would be highlight
Note: 2019 is not only IUPAC's centenial, but the 150th anniversary of the periodic table
NSF places high value on educating students to be leaders and innovators in emerging and rapidly changing STEM fields as well as educating a scientifically literate populace. In pursuit of this goal, IUSE: EHR supports projects that have the potential to improve student learning in STEM through development of new curricular materials and methods of instruction, and development of new assessment tools to measure student learning. I
item 1
dictionaries and hierarchies
T11 I am assuming dictionaries are Compendex and Reaxys Index terms. Are there others, and what do we mean by hierarchies. Taxonomies?
Let’s now go back to the initial list of options(Fig.2.2
What is the shortcut for doing this. I can't find a breadcrumb or trail, and the back arrow does not go there. I can click Quick search, and redo the search, but there must be a better way.
AND –although terms entered without any operator are interpreted as AND
How close do the words need to be? I assume in the same document, or "record", if this is done in substance or reaction records.
Summary
I am thinking that this document should be covered first, before the structure search document. At least some aspects of this would have been useful to have covered prior to the first document (File 5)
nd/orprepositions
I am not sure what you mean by this. In the next statement you say OR, but here you say "and/or".
may
are we editing this for "American" English? I would think "can" instead of "may" is better
eaxys uses severalhundred algorithms to interpret the queryand directly gives answers that may be in Document, Substanceand/or ReactionRecords
Is there a place where further documentation on this can be found. I have Thibault's article from the ACS symposium series book, and will look this up there.
and we may want to review all reactions regardless of whether yields are quoted.
So if a yield is not reported, the planner will not show it unless you set this to zero % yield, right?
3.3 Initial observations of UALR student use of h. annotations concurrent with Drupal comment
My thoughts on h.
Toxicological InformationToxicological InformationHeptatoxicity
Second try
Toxicity Summary
Use of hypothes.is in literature search, here I am linking to PubChem LCSS section on Nicotine
This video shows how one could use the ability to aggregate annotations at the bottom of a page to prepare for in-class lecture.
This video shows how hypothes.is annotations was used in flipped classroom lecture preparation.
Chemical informatics for facilitating international collaboration This activity aims at creating a working group of scientists to collaboratively source, collate, and analyse data with unique chemical signatures. It seeks to compile data collected from a broad range of routine chemical monitoring activities that contain chemical signatures (e.g. data collected from atmospheric monitoring, environmental sample collection, water testing, and more). The intent is to connect chemical and information scientists from different regions of the world to create a hub in which the information can be disseminated to the collaborators for visualisation and informative analysis of global and regional chemistry. This work is intended to facilitate engagement of the Technical Secretariat with the scientific community. Main output will be a data collation centre serving as a hub for collating and reducing data into formats compatible with the analytical tools used by the collaborating researchers. The hub, located in one of the participating universities, will support the network of collaborating scientists and build its capacity to expand beyond the implementation period.
I believe a small EU grant has been awarded to look into this, although the funds are not available for us, we could support this, and piggy back off of it.
*fulleren*
Note, you can't use stars, but need to use the "contains" option
EMTREE drug terms listed in the Index Terms
EMTREE is like Mesh, but how do you get to the index terms, Unfortunately, h. will not link inside of Reaxys, and so I can't give a link to where I am
Get the full record (in XML) of CIDs that have the substructure “C3=NC1=C(C=NC2=C1C=NC=C2)[N]3”
Once again, I am not clear on how to read this file, https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsubstructure/smiles/C3=NC1=C(C=NC2=C1C=NC=C2)[N]3/record/xml
identity search.
For similarity search, use, https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/cid/334/cids/txt?Threshold=95
Getting molecular properties of a set of compounds
It seems most of the things we can get are from the advanced search (entrez?) options. Can we get other items, like boiling points?
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CSCPPACGZOOCGX-UHFFFAOYSA-N/record/XML?record_type=3d
How do you read this file? Can you pull a mol file from it?https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CSCPPACGZOOCGX-UHFFFAOYSA-N/record/XML?record_type=3d
PubChem subgraph fingerprints,
Why are these called a "Subgraph"? I see this from , wikipedia. Is it that each bit of the fingerprint represents a subgraph of the molecule, which in it self is the graph? That is, its existance/nonexistance of this subset within the entire?.
without minor isotopes by combining the retrieved search results [from (a)] with the following Entrez indices:
once you have done this, click on the number of hints, go to the doc sum page, go to advanced, and use the advanced query builder to perform the filters.
? [Note that a compound may have multiple EC50 values determined from different experiments (likely under different experimental conditions)
There are two ways to get rid of duplicates. You can simply paste the CIDs into the pubchem search, and search, I think this requires Chrome.
or
You can go to Data/data tools in excel, and choose the "Remove duplicates" tool
To perform an identity search for Cymbalta (CID 60835), go to the Chemical Structure Search pag
so if many CIDs relate to specific isotopes, do the normal molar masses use ave values, like the periodic table?
PubChem Search
the beta search link of the homepage
PubChem Chemical Structure Searc
Direct Link is Under Services on the homepage
EC50”
Half maximal effective concentration (EC50) refers to the concentration of a drug, antibody or toxicant which induces a response halfway between the baseline and maximum after a specified exposure time
s. Click the “Pharmacological Actions” link under “BioMedical Annotation” to choose the c
Note you get 2 hits, the search 5090 and 5472495. This tells you that there is a molecule that is 80% similar and has been tested as active.
n, use the smallest EC50 value (for simplicity) if there are multiple values
Is there a quick way to recognize duplicates in Excel? In the case of CID5152, the compound CID9892481 was repeated 3 times
mentioned at the top of t
444036 is now getting 5 targets
What is the difference between the non-common components of the compounds in (a)?
Is there a quick way to compare smiles to do this?
Provide the query CID in the search box and run the search. Repeat the search with the “same isoto
note in the query, this gives #24 and #23, which in the advanced search,
A quick scan showed only 1 covalent unit in -24, so was -23 done just because it is good practice?
Also, the entrez history shows here too.
Also, in the first search with 56 results, the first three did not have isotopes specified, while in the seconds search, those were the only ones to come out. Does it always give priority in the search to ones without isotopic labels?
This leads to a bigger question. are the molar masses from the periodic table, or are they related to specific isotopes?
2.1. The Structure Clustering tool
Private note - useful for GHS?
this URL
Available through the services menu of PubChem homepage
1 SimilarityCoefficients
Good description of similarity methods
PDB and CSD
PDB is biological compounds while CSD is material sciences oriented.
How many compounds
Use OR Bolean in advanced search
How many compounds in
Use "AND" of advanced search, the above classification browser results will be in search history
For example, the protein-bound 3-D structure of penicillin V can be accessed via the following UR
This can be done from PubChem TOC of Classification browser, Biomolecular Interactions and Pathways and Protein Bound 3-D Structures The next link is same, but Chemical and Physical Properties/Crystal structures
ummarize what Lipinski’s rule of 5 i
</= 5 H Bond donors </= 10 H Nond acceptors </= 500 Daltons LogP </= 5
the “MeSH Synonyms” se
This chemical has depositor supplied syntony P071 fro AK Scientific,P071
While Cetrizine has Mesh synonym of P071
zyrtec[completesynonym
exact name match (zyrtec-D will not work, it is a partial match)
t is the CID of that covalent-bonded unit? [A covalently-bound unit (or simply called covalent unit) consists of a group of
note, two of these are mixtures, which could be filtered out by setting covalent units to 1:1
The use of covalently bonded units (instead of components) removes this ambiguity because it is well accepted that NaCl is bonded through an ionic bond.)
sodium chloride comes up with 1:2 not 1:1 covalent units.
zyrtec
gets MESH and Depositor supplied synonyms
grouping
group
These conformer models aim to generate bioactive conformers,which would be found in protein-ligand complexes. For this reason, these conformers are often very different from their experimental structures determined in the gas phase
How do you choose which are best? Both, from the perspective of creating them for the databank, and for using them as a client (in your research).
following condition
https://www.ncbi.nlm.nih.gov/pubmed/21933373 https://www.ncbi.nlm.nih.gov/pubmed/21272340 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702940/
n the ST-optimization approach, the shape overlap between the molecules (that is, the ST score) are maximized and the single-point CT score is evaluated at that superposition. On the contrary, the CT-optimization considers both ST and CT scores to find the best superposition between molecules, and the single-point ST score is computed at that superposition
Can there be some sort of superposition using an algorithm that is sort of in the middle, maximizes both ST and CT?
here NAand NBare the number of bits set in the fingerprints for molecules A and B, respectively, and NABis the number of bits set in both fingerprints.
Is there a service that generates fingerprints from smiles strings?
ubChem uses its ownfingerprint called PubChem subgraph fingerprints.
If you follow the link you see the fingerprint key, and this is confusing. How would you represent a molecule with on carbon, 1 oxygen and 2 hydrogen (formaldehyde) when the lowest C count is 2, and H count is 4
choose adesireddegree of “sameness” from several predefined options. To see these options, one need to expand the options section by clicking the “plus” button next to the “option” section headin
I get confused between indices and filters. If you open the filters, you see what I thought were Indices, (HBD,HBA,...).
Also, what is the criteria for similar structures? I don't see a 90%, 80%,....
PubChem Searc
"Try PubChem Search Beta" from homepage
PubChem Chemical
Under Services of homepage
f the query is a phrase or a name with non-alphanumeric characters, double quotes should be used around the query.
text searches with numbers, should use double quotes
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pccompound (for Compound) http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pcsubstance (for Substance) http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pcassay (for BioAssay).
These links are the same as the above section on indices
retrieved in the XML format, using the eInfo functionality in E-Utilities (which will be covered in Module 7):
to open these xml files in Google sheets use: =importxml(A1,"//Field/FullName") where in A1 you place the link below
For numeric indices, a search for a range of values can be done by using minimum and maximum values separated by a colon and followed by the bracketed index name (e.g., “100:105[MolecularWeight]”).
use of numeric indices X:Y
PubChem Compound:
PubChem Indices
BondChiralCount [BCC, BCCNT]: Total count of chiral bonds in a given compound, integer. BondChiralDefCount [BCDC, BCDCNT]: Total count of defined chiral bonds in a given compound, integer. BondChiralUndefCount [BCUC, BCUCNT]: Total count of undefined chiral bonds in a given compound, integer.
I am confused on what is a chiral bond. I thought enantiomers (chiral molecules) had chiral atoms, not bonds. Are cis/trans isomers chiral bonds? If so, the boiling points are different, and enatiomers have the same boiling points, right? So what is a chiral bond?
Test Account A "test" account enables you to upload data into the pending submissions database, but does not enable you to "commit" the data into the official PubChem database. The test account is just for trying the system to determine if you can successfully upload and see your structure. When you register for a test account, you must enter your e-mail address. When you go to the next screen, PubChem upload will send a message to your e-mail address with a code that you must enter on the second screen in order to proceed. This confirms the validity of the e-mail address, in order to ensure communications about your PubChem submissions. When you are read
test account
thasSOlongbeenacustomtoprefaceacourseoflectureswiththehistoryofthesciencewhichistheirsubject,thatitmaybenecessarytostate,briefly,thereasonsthathaveinducedmetodepartfromthisestablishedusage.
This is a test of a Gutenberg Archive book uploaded to the OLCC
EXPERIMENTSANDOBSERVATIONS
This is a test of the Gutenberg archive
might fail if API is not available# query common namey1 <- ci_query(c('Formaldehyde','Triclosan'), type ='name')names(y1)str(y1[['Triclosan']]) # lots of information insidey1[['Triclosan']]$inchikey# Query by CASy2 <- ci_query('50-00-0', type ='rn', match ='first')y2[['50-00-0']]$inchikey# query by inchikeyy3 <- ci_query('WSFSSNUMVMOOMR-UHFFFAOYSA-N', type ='inchikey')y3[[1]]$name# extract lop-Psapply(y1, function(y){if (length(y) == 1 && is.na(y))return(NA)y$physprop$Value[y$physprop$`Physical Property`=='log P (octanol-water)']})## End(Not ru
this is the code but add
P370+P378
what does it mean to have two P codes added together
t the approach above is easily implemented andcan run in a wide range of environments. It has the benefitof synergy with the c
test for public file on cheminformatics OLCC
es.PubChem archives the molecular structure and bioassay data from the MLSCNand other contributors. PubChem provides search, retrieval, and data analysistools to optimize the utility of these results. PubChem further enhances the re-search utility of the
Restricted Access Article - I am testing to see if this link works when someone is logged in, and is not logged in, to the OLCC course.
Spelling correction
Are mispelled words common in patents? I know someone who thinks they are done intentionally. Cheers, Bob
Amino Acid Properties Thermodynamic Properties of Pure Substances
bad links
The metadata, data, comments and any processing errors are stored in an array in PHP and then converted to XML and saved. Figures 4 and and55 show a comparison of the original JCAMP file (e.g. “../spectra/view/000000115/JCAMP”) and JCAMP saved in XML (e.g. “../spectra/view/000000115/XML”).
this is to show you something
ol-water partition coefficient (ClogP). The descriptors tend to convolute any different properties into these simple scalar descriptors, but can be highly effective in certain circumstances and are widely appreciated for their interpretability in interactive systems. One such set of property descriptors that has gained wide acceptance is the Lipinski rule-of-five, which has been suggested as an heuristic for indicating the oral absorption of a potential drug based on marketed orally-dosed drugs. The rule-of-five applies four calculated properties and defined cut-offs
test of tags
Morgan algorithm initially developed by Gluckat DuPont (Wilmington, DE, USA) and adapted byCAS.55
How is the Morgan algorithm developed, and are there alternatives?
Most distinctive interactions occur between vitamins and medicines curing ailments of classes such as central nervous system or dermatological in nature. Several less similar interactions filtered as distinctive, include compound pairs from distinct classes. Figure 6i,
Note how we can use hypothes.is to link anywhere in an article, and discuss it.
ted to share with you all my project that I am working on here at Centre. During my ti
yrdy
To automate functions on chemical data, the data structure needs to be systematically defined and consistently applied.
Who is responsible for the systematic definitions of data structure and their consistent application?
uick searchin Reaxysallows you to combine structure and text searches. Try doing the searc
How do you turn on quicksearch
Issues with Intelligent Search Engines
Damon, I am not sure you are familiar with Hypothes.is, but we will be using this, and I think the first iteration of a learning assignment should be from the expert, which can then get dumbed down to multiple levels, depending on student abilities. So we can expect an iterative process.
SearchforpropertiesusingtheSearchpropertiesfieldandDrag&Drop
this is an experiment for a file uploaded to a web page
St Joseph Aspirin-Free
S,
Please note that a pubchem search of aspirin give acetaminophen because there is a depositor-supplied synonym called St. Joseph aspirin-free.
I am posting this annotation public, but it could be posted to a class discussion, that sends an email to everyone in the class when the annotation is made
that is, a string of 0’s and 1’s). The position of each number in this string corresponds to a particular fragment. If the molecule has a particular fragment,
Do XYZ using the tanimoto coef.
Molecular similarity methods can be broadly classified into two-dimensional (2-D) and three-dimensional (3-D) similarity methods. Typically, 2-D similarity methods use so-called molecular fingerprints, which encode structural information of a molecule into a binary string (that is, a string of 0’s and 1’s). The position of each number in this string corresponds to a particular fragment. If the molecule has a particular fragment, t
Using tanimoto coefficient compare the two molecules on your list
Open Data in Chemistry. One can obtain all scientific data in the public domain when wanted and reuse it for whatever purpose.• Open Standards in Chemistry. One can find visible community mechanisms for protocols and communicating information. The mechanisms for creating and maintaining these standards cover a wide spectrum of human organisations, including various degrees of consent.• Open Source in Chemistry. One can use other people's code without further permission, including changing it for one's own use and distributing it again.
Assignment 2: Relate ODOSOS to Open Notebook science in 500 words or less
BioAssays, Tested (24) Compounds identified as tested in screening experiments BioActivity Analysis of reported tested compounds Protein 3D Structures (5) Compounds bound to proteins in atructure biology experiments Crystal Structure Of The Complex Of Goat Lactoperoxidase With Acrylonitrile At 1.98 A Resolution (1)Crystal Structure Of Thermolysin In Complex With Aniline (1)Gspb (1)... All 14 Structures BioMedical Annotation Pharmacological Actions (24) Therapeutic use and National Library of Medicine (NLM) compound classifications Carcinogens (24)Mutagens (5)Solvents (1)... All 13 Pharmacological Actions BioSystems (10) Compounds involved in biological pathways Depositor Category Chemical Vendors (24) NIH Molecular Libraries (21) Find related data Database: Select BioSystems Gene MeSH Nucleotide OMIM PMC Protein PubChem BioAssay PubChem Compound PubChem Substance PubMed Structure Taxonomy Option: Find items Search details (#4) AND 82002273[PharmActionID] Search See more... Recent activity Clear Turn Off Turn On PubChem Compounds from Classification for pchierarchy (Select 185... (907) PubChem Compounds from Classification for pchierarchy (Select 1857072)Search PubChem Compound Disciplines and Occupations Category Disciplines and Occupations Category MeSH PubChem Compounds from Classification for pchierarchy (Select 216... (2888) PubChem Compounds from Classification for pchierarchy (Select 2166072)Search PubChem Compound Your browsing activity is empty. Activity recording is turned off. Turn recording back on See more... You are here: NCBI > Chemicals & Bioassays > PubChem Compound Support Center <img alt="" src="/stat?jsdisabled=true&ncbi_app=entrez&ncbi_db=pccompound&ncbi_pdid=docsum&ncbi_phid=396C196A86FF0E210000000000D90061" />
What are bioassays
Element Use
what are element uses
ClinicalTrials.gov
What are clinical trials?
Supervised learning
is this really supervised
Builder
When I click "All Fields" a lot of options come up, ranging from ActiceAidCount to XlogP. Are all of these Entrez indices? (some being text, and some being numerical?
olcc
ith this page you can draw a structure in 2D, compare that with its 3D structure, and also see its structural data in a variety of form
does asprin show here
Contributors can specify a ‘hold-until date’, until which the contributed data will not be visible to the public.
On the PubChem Datasources page, there are 6 data types, https://hyp.is/G504wMLkEeafGh_HgqKgaQ/pubchem.ncbi.nlm.nih.gov/sources/
If you go to Nature Chemical Biology, they have 9,424 live substances and 131 on hold substances.
So does that show up twice in the above link, where there are 444 live subtance and 5 on hold substance data types?
Data submission using PubChem upload
2017 Cheminformatics OLCC students are responsible to read this section on PubChem Upload. Further information is available at the Upload Help Page, https://pubchem.ncbi.nlm.nih.gov/upload/docs/upload_help_complete.html
Data TypeLive Substances(444)Live BioAssays(81)Annotations(50)On Hold BioAssays(10)Classifications(7)On Hold Substances(5)
This is confusing. What are the onhold Substance and Bioassays? I will link to this from the article, http://nar.oxfordjournals.org/content/44/D1/D1202.long, but it seems that data submission using pubchem upload, a data source may have some data on hold, and other data live.
Mesomerism Mesomerism is the concept related to the situation in which the molecular structure cannot be unambiguously represented by a single classical structural formula; rather, two (or more) mesomeric structures must be drawn and considered to contribute to the overall picture. As the IUPAC Gold Book states, “mesomerism” is “Essentially synonymous with resonance. The term is particularly associated with the picture of π-electrons as less localized in an actual molecule than in a Lewis formula. The term is intended to imply that the correct representation of a structure is intermediate between two or more Lewis formulae” [28]. In other words, mesomers are considered as imaginary objects (or even drawing artifacts) that cannot be distinguished by a simple chemical identifier. Mesomerism is effectively eliminated in InChI. Mesomers have the same InChIs (this is true for all possible InChI layouts of layers). Actually, this is very natural. Mesomeric structures of a molecular entity have the same basic connectivity but differ in bond orders, and maybe by having atomic charges on different atoms. InChI does not use bond orders and does not place charges on particular atoms; the placement of hydrogen atoms in a mesomeric system, which would be important for InChI, is always the same.
In class yesterday we covered mesomerism with canonical SMILES, tomorrow you need to be prepared to explain how InChI covers this for the molecule you used in class yesterday, and be prepared to lead a discussion with your group on the differences between the two methods.
GHS Classification
Class, in section 12.1.1 you see the GHS safety codes for acetone and at the bottom of this section you get links to original sources. These include the International Labor Organization, European Union, HSIS of Australia and the Japanese National Institute of Technology. Your assignment is to compare these four sources of GHS Hazard Statements for Acetone, and be prepared for an in-class discussion on OSHA's Hazcom 2012, https://www.osha.gov/dsg/hazcom/ghs-final-rule.html and specifically appendix c https://www.osha.gov/dsg/hazcom/appendix_c.pdf
e-Science-4th Paradigm:
This is the future of science!
Smallest number indicates limiting reagent.
You are half way through the mole-to-mole step, where you would place on the numerator the stioichiometric coefficient of the compound you want to solve for.