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Questions tagged [cheminformatics]

Cheminformatics involves the production, processing, filtering, and searching of chemical information. This includes chemical databases, computational screening, searching, etc.

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Number of stable molecules [closed]

Is there are software/freeware (artificial intelligence or whatever) that given some types of atoms and their number how many "stable"/"reliable" molecules we can build involving ...
Vincent ISOZ's user avatar
-3 votes
0 answers
27 views

Organic Rest verification in Cheminformatics

So I am using SMARTS-Pattern to find molecules that have certain functional groups / properties. As a simple example lets take an Aldehyde. Structurally is R=O - i can match this with a pattern of &...
fwieland's user avatar
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Seeking Comprehensive GHS Hazard Database for Chemicals

I have been using PubChem as a source for GHS hazard information, but I have noticed that the database is incomplete for some chemicals. While PubChem is a great resource, I am looking for a more ...
Noushin Omidvar's user avatar
2 votes
1 answer
47 views

What does ‘S/A’ mean in SMARTS pattern when using Chemicalize to draw the chemical structure?

I am still new to the SMARTS annotation. I am wondering what does S/A’ mean on the bond labeling drawn with Chemicalize using SMARTS [!#1]c1n[cH]nc([!#1])c1[!#1]? ...
tassaneel's user avatar
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3 votes
1 answer
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What does ‘(A)’ mean in SMARTS pattern when using Chemicalize to draw the chemical structure?

I am not quite sure what ‘(A)’ could mean for the carbon atom when writing the SMARTS CCN(C)C using Chemicalize to draw the chemical structure below. Can anyone ...
tassaneel's user avatar
  • 131
4 votes
1 answer
201 views

More potent caffeine analogs (in silico study)

Is it possible to do a Structure Activity Relationship for caffeine given that its structure is similar to that of adenosine? Maybe more potent analogues can be made using caffeine as lead compound? ...
C418's user avatar
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0 answers
80 views

Reaction SMARTS for Secondary Amine and Carboxylic Acid

I'm working on replicating methods from Klarich et al. [1] and the authors do not provide the reaction SMARTS used for synthesizing secondary amine + carboxylic acid building blocks. Does anyone have ...
Karl's user avatar
  • 125
1 vote
1 answer
84 views

Give a molecule, how do we determine the serial number of each atom in it to put in a pdb file?

Example: For molecule of 1-chloro-4-nitrobenzene, using RDKit's MolToPDBFile() function, I can convert this molecule to the pdb file shown below. ...
Yuuya's user avatar
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0 answers
30 views

How to integrade a group of disconnected smiles descriptors from molecular into a single smiles descriptor?

I am new to cheminfo so this question may sound stupid. I am trying to calculate the RDF(radial distribution function) of these two compounds below: https://pubchem.ncbi.nlm.nih.gov/compound/155293646 ...
Yuuya's user avatar
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-1 votes
1 answer
52 views

Multidimensional Chemical Space - nD coordinate system

I have a dataset of many organic compounds. I would like to describe them using a set of coordinates. A 2D example of what I want to do is chemplot, this package lets you create a 2D coordinate system ...
Mirko's user avatar
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0 answers
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HOMO and LUMO energy levels diagrams

Good time of day. I want to draw the same beautiful pictures in my work as I will attach below taking from some articles. Are there any programms or scripts which can do this? I would be glad if ...
UserIn's user avatar
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0 votes
1 answer
111 views

What is the SMARTS string for a benzene ring (any substitution pattern)

I would like to use RDKit to highlight all benzene rings (regardless of substitution pattern - e.g. phenol, chlorobenene, benzoic acid type should all be highlighted) in any given molecule. I cannot ...
user avatar
3 votes
1 answer
365 views

Problem adding non-polar hydrogens whilst converting from pdbqt to pdb

I'm using OpenBabel 3.1.1 and the Python to C++ bindings to load pdbqt files and convert them to pdb with explicit hydrogens. Unfortunately, I can't add nonpolar hydrogens using OpenBabel. I can do ...
Anthony Nash's user avatar
-1 votes
1 answer
351 views

Transform raw atomic coordinate data into SDF file

I have raw data of the atom types and their coordinates. For example, water molecule is: O -0.034 0.977 0.007 H 0.064 0.020 0.001 H 0.871 1.300 0.0006 Here, I ...
neco's user avatar
  • 115
5 votes
2 answers
314 views

Two compounds (not stereoisomers) have same SMILES code

Are there compounds that have the same SMILES code but are not stereoisomers? I am trying to find inconsistencies with SMILES code and currently I have that many compounds have multiples options for ...
xboxbot's user avatar
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2 votes
1 answer
117 views

Difference between two forms of benzothiadiazole [closed]

Can someone please advise / point me to information regarding the difference between these two compounds: https://www.combi-blocks.com/cgi-bin/find.cgi?HC-3087 https://www.combi-blocks.com/cgi-bin/...
user6376297's user avatar
-2 votes
1 answer
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Substructure abbreviations with the SMILES format

I am trying to use the SMILES format for encoding molecules from handwritten logbooks. The molecules often contain abbreviations, such as "Ph" for a Phenyl group. Is there a way to have ...
finlay morrison's user avatar
0 votes
0 answers
118 views

How does the canonization method of RDKit operate when valence is exceeded?

RDKit's canonization method1 allows nitrogen to bond with 3 hydrogen atoms and one oxygen atom ...
nightcod3r's user avatar
4 votes
0 answers
148 views

Molecule similarity measurement

I'm not a chemistry specialist, I'm more from informatics, and I have a question concerning molecule similarity measurement. Let's taking these two molecules: mol1: c1(cccnc1)C(O)=O mol2: O=C(O)...
user12910's user avatar
  • 141
5 votes
1 answer
2k views

How to convert SMILES to 3D (with higher accuracy than RDKit)?

I am interested in assigning 3D coordinates to (atoms in) some 10K molecules that I have, currently represented by SMILES. This is because as have been shown by many chemoinformatics papers, 3D and 2D ...
jasperhyp's user avatar
-1 votes
1 answer
89 views

"Best" way of referencing chemicals in databases [closed]

What is considered the "best" way of referencing chemicals in a database ? As far as I understand CAS nr. is a specific type of hash whereas something like smiles stores structural ...
Julien's user avatar
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2 votes
2 answers
221 views

Open MSDS (GHS/CLP) database API by CAS#

I am looking for an open API to a database that provides GHS/CLP classifications. I am aware this is a duplicate, however the post in question never provided an answer since, as far as I can tell ...
Julien's user avatar
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1 vote
0 answers
219 views

Defining SMARTS reaction template

I want to have a reaction template involves combination of 2 radicals such as this one O=C1CCC(=O)[N]1.[H]>>[H]N1C(=O)C([H])([H])C([H])([H])C1=O. A generic ...
jayjay's user avatar
  • 309
4 votes
1 answer
285 views

Line Entry system like SMILES for metals?

SMILES is not designed for metallic compounds. Is there a similar ASCII line entry notation for metallic compounds, including repeating structure in space, &c.?
Sam's user avatar
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5 votes
1 answer
807 views

Rotating molecule representations with rdkit

I'm trying to display some molecules in rdkit and save them as png files. Simple enough. However, when I display them, most of them are drawn at a weird angle (shown below) or even completely upside ...
apvn's user avatar
  • 75
1 vote
1 answer
1k views

accessing the ZINC15 and ZINC20 databases

I'm trying to access the ZINC15 and ZINC20 databases but I've been at it the whole morning and I can not figure out how to do it. I am not that experienced with programming so maybe there's something ...
apvn's user avatar
  • 75
3 votes
1 answer
239 views

Python implementation of the Lilly Medchem Rules code? [closed]

As the title suggests, I am looking for a Python implementation of the Lilly filter from the paper: https://pubs.acs.org/doi/full/10.1021/jm301008n. The shared code on GitHub (https://github.com/...
mac179's user avatar
  • 319
3 votes
1 answer
512 views

SMARTS: distinguish between alcohol and carboxylic acid

I'm new to SMARTS and have to identify substructures with the Python package rdkit, so far so good. Let's say I have a SMILES with an carboxylic acid and a alcohol ...
dideldideldum's user avatar
0 votes
1 answer
129 views

Are there tools or algorithms to detect organic molecules from 3D crystal structures?

The task I'm thinking of is to detect entire molecules from structures, such as in a crystallographic information file (CIF) or from the XYZ file generated in a molecular dynamics simulation. ...
QGent's user avatar
  • 176
1 vote
0 answers
182 views

SMILES vs. Graph for generating molecules

I have seen this question, but mine is slightly different, focusing on generating molecules. There are many published methods for generating molecules; some of which generate SMILES and others ...
Hossein's user avatar
  • 111
4 votes
1 answer
4k views

How to use Python RDKit to remove stereochemistry, salts and molecules with undesirable atoms or groups?

I am not a chemist, I come from a computer science background. Bung et al. [1] say in the Data preprocessing part that they used Python RDKit to remove stereochemistry, salts, and molecules with ...
mac179's user avatar
  • 319
2 votes
1 answer
2k views

Python and RDKit to extract sub-structures in a SMILES

I am not a chemist, I come from a computer science background. I am involved in a cheminformatics project. I have a list of molecules in SMILES format, which I want to extract sub-structures from. I ...
mac179's user avatar
  • 319
0 votes
0 answers
72 views

Machine learning-based drug design: how to determine the desired properties given a target?

I am working on a machine learning-based drug design project. The machine learning part was easily understood for me being from a computer science background. However, the biochemistry part is what I ...
mac179's user avatar
  • 319
4 votes
1 answer
136 views

Forming conjugate acid of borate anion via protonation

I am a biologist so please forgive me as I likely won't be as rigorous as a professional chemist. I am using the RDKit package to extract organic molecules from salts, where one ion is organic and the ...
atevm's user avatar
  • 151
1 vote
0 answers
660 views

Is chemAxon check of validity of a smiles the same as RDKit check?

I am working on an AI-based drug design application, I want to verify the validity of the produced molecules (which are in smiles representation). I found a solution to this using the RDKit library ...
mac179's user avatar
  • 319
7 votes
1 answer
751 views

Listing all possible structures for a given Markush structure automatically

I have Markush formulas described as mol blocks, v3000, even if that does not matter that much because I could convert it into another format if needed. I need the possibility to automatically list ...
bfalk's user avatar
  • 73
1 vote
0 answers
59 views

Handling of tautomerism in QSAR modelling

This article from 2009: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776169/ mentions the potential impact of tautomerism on QSAR modelling, and concludes that more work is needed to address it. 12 ...
user6376297's user avatar
-1 votes
1 answer
1k views

How to get smiles from pubchem CID

I have downloaded about 10k compounds of interest from pubchem. Im using pubchempy to get smiles for all those structures . I am able to get smiles for each compound one by one but while fetching two ...
vemaparna's user avatar
5 votes
1 answer
593 views

SMARTS pattern for amines with connected carbons only having bonds to carbon or hydrogen

I'm trying to find a SMARTS pattern that matches primary and secondary amines, where the connected carbon atoms only have connections to other carbon atoms or hydrogens (to exclude amides, guanidines, ...
snurden's user avatar
  • 1,449
3 votes
1 answer
263 views

What Chemical Database Extensions for Structure and Similarity Search are there?

I am looking for extensions/add-ons for relational databases (RDBMS) that enable storing and handling chemical structures including the possibility for substructure searches and similarity search. I ...
buddemat's user avatar
  • 235
2 votes
2 answers
974 views

How to highlight the substructure of a molecule with thick red lines in RDKit as SVG (high res)

I have the following code: ...
littleworth's user avatar
4 votes
2 answers
178 views

Why do two programs assign different SMILES to one amino acid sequence?

I have an amino acids string "MKGK" and I would like to convert it into SMILES format. I tried two approaches. First with PepSMI which gives me: ...
littleworth's user avatar
5 votes
1 answer
223 views

What do sequence numbers in PDB files actually mean and why don't they match the sequence?

I am studying the 3D structure of the LDH from x-ray crystallographic imaging I was pointed to from Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry ...
Gunther Schadow's user avatar
0 votes
1 answer
60 views

Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry showing both reactant ligands?

I am desperately searching for an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactose synthase -- we have ...
Gunther Schadow's user avatar
1 vote
0 answers
123 views

What is an enzymatic reaction for which a detailed tertiary structure showing all ligands is available on the PDB?

This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate ...
Gunther Schadow's user avatar
2 votes
2 answers
139 views

How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
Gunther Schadow's user avatar
2 votes
1 answer
454 views

How to "draw" a coordination bond (dashed bond) in MOLFILE?

How can we "draw" a coordination bond (dashed bond) in MOLFILE? I cannot find a bond property or option that would allow me to choose such a thing. So many drawings of organo-metallic ...
Gunther Schadow's user avatar
1 vote
0 answers
42 views

Classification model from biological assays with different compounds

If I want to use an undersampling approach to construct the machine learning model (classification model predicting whether the target compounds are active or inactive, using chemical fingerprint as ...
tassaneel's user avatar
  • 131
5 votes
1 answer
216 views

InChI issue with organic salts, inconsistent approach?

I am wondering why there is the following inconsistency in InChI: penicillin G vs. penicillin G potassium salt uses the /p layer to drop a proton but chloramine-T vs. tosylchloramide drops an H from ...
Gunther Schadow's user avatar
3 votes
1 answer
198 views

How to implement SDF format?

I have a program that returns a file with SDF format molecule. Now I want to transfer it to SMILES with Open Babel. But I don't get the result I expect. I have visited different websites that show how ...
Tim Schneider's user avatar

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