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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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 ...
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-1 votes
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What is the best way to measure similarity between molecules of the same formula? [migrated]

I have enumerated a large set of carbocations all of the formula C10H17+, all of course with differing structures. I know there are many different approaches of computing similarity between molecules, ...
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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. ...
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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 ...
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Cheminformatics resources? [duplicate]

Like the title says, I'd be interesed in learning some cheminformatics (not computational chemistry) workflows but there seems to be quite a shortage of up to date tutorials/books. A lot of papers ...
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2 votes
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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. I was reading the following paper: https://www.future-science.com/doi/suppl/10.4155/fmc-2020-0262. The authors say in the Data ...
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2 votes
1 answer
243 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 ...
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How to choose descriptors for QSAR/QSPR?

I would like to carry out a QSPR study with ionic liquids. After reading the QSAR/QSPR literature, I am a bit confused on how should I choose molecular descriptors. There seem to be a lot of options, ...
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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 ...
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3 votes
1 answer
81 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 ...
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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 ...
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7 votes
1 answer
143 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 ...
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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 ...
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-1 votes
1 answer
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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 ...
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5 votes
1 answer
131 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, ...
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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 ...
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2 answers
260 views

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

I have the following code: ...
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1 vote
1 answer
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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: ...
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5 votes
1 answer
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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 ...
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1 answer
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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 ...
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1 vote
0 answers
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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 ...
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2 votes
2 answers
118 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 ...
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2 votes
1 answer
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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 ...
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1 vote
0 answers
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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 ...
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5 votes
1 answer
168 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 ...
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3 votes
1 answer
110 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 ...
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6 votes
1 answer
213 views

Can cis-trans isomers have same InChI?

From all we know only tautomers should get the same InChI key, or, in case of the second block, if there are lots of stereo centers. However these cases are just collisions, they still have different ...
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6 votes
1 answer
143 views

Discrepancy when calulating mol weights with ChemSketch and Python RDKit

I am an IT guy with little knowledge of Chemistry, so please bear with me... For context: I am working with a system that has a lot of structures, their .mol files ...
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5 votes
1 answer
415 views

How to find the largest cyclic substructure with RDKit?

I have a bunch of structures and of each I would like to find the largest cyclic substructure. I'm not a chemist, so I don't know if there is a common terminology for this. I hope, I made it clear ...
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4 votes
0 answers
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Why is the reported melting point of formaldehyde so different from the triple point?

All of the (believable) sources at PubChem and most of the sources at NIST give 181 K for the melting point. The one source I can find for the triple point is NIST, which gives 155 K. There are two ...
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12 votes
3 answers
946 views

Does the SDF format have any benefit over SMILES?

The eMolecules page for example offers a complete dataset containing ~26 million structures. They're providing it either as a 300 MB SMILES archive or 6 GB SDF archive (1.5 GB and 50 GB uncompressed ...
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2 votes
1 answer
128 views

INCHI-1 software input format(s)?

I am looking at the latest INCHI-1 software which supports molecules with 32 thousand atoms. I work with macro-molecules and want to use that to generate humongous InChIs. I've never used that INCHI-1 ...
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6 votes
1 answer
86 views

Are atom coordinates in molfile necessary to produce a valid InChI identifier

I took this molfile of benzoic acid: ...
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6 votes
0 answers
224 views

Are there any ADME predictions tools available for Python/RDKit?

Is there any Pythonic way (a.k.a: a module, an rdkit package, etc) or an API I can use for ADME predictions? I need to prioritize some compounds for purchase/synthesis and some sort of ADME scoring ...
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4 votes
1 answer
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How to draw xenon hexafluoride in rdkit from SMILES?

In SMILES I would think that $\ce{XeF6}$ would be F[Xe](F)(F)(F)(F)F or F[Xe](F)(F)(F)(F)(F). A quick Wikipedia search showed ...
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2 votes
1 answer
156 views

SMART string for alkyl group excluding alcohols

I'm quite new to the usage of SMARTS strings. I would like to find all alkyl groups (but no $\ce{CH3})$ in a component, here e.g. cyclohexanol (C1CCC(CC1)O). My ...
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1 vote
0 answers
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Are molecular properties robust towards manipulations? [closed]

Machine learning algorithms analyze molecules by looking at their molecular representations (e. g. SMILES and graph) and turning them into feature maps that help the algorithm to distinguish them. In ...
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7 votes
1 answer
109 views

Using RDKit to determine "nonring, nonterminal atoms"

I am a non-chemist using RDKit to determine the number of "nonring, nonterminal atoms" in a molecule. I can't find anything in the RDKit documentation that helps with "nonterminal"....
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8 votes
1 answer
298 views

Using RDKit to count "RR, the number of rigid single or fused ring systems in the molecule"

I am a computer scientist, not a chemist, working with RDKit. I need to compute something described to me as "RR, the number of rigid single or fused ring systems in the molecule." I know I ...
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3 votes
1 answer
112 views

Best Cheminformatics API for drawing SMARTS reactions?

I have a need to automatically draw SMARTS reactions. Rdkit's drawings are suboptimal. OpenBabel's drawings don't work properly on macOS. Indigo's drawings are cut off half the page. I would love to ...
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3 votes
2 answers
180 views

Why don’t we have a list of all compounds yet?

With only three basic particles making up atoms, and their interaction fairly well understood (we can even predict the chemical properties of elements we have not yet discovered) atoms seem to be like ...
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3 votes
0 answers
61 views

SMARTS string matching an aldehyde or a ketone where the target alpha carbon is less substituted than the other carbon

I need a SMARTS string that matches the following critereon: It makes an aldehyde or a ketone only The target carbon is an alpha carbon The other alpha carbon must be more substituted (or be an ...
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3 votes
1 answer
145 views

Representing conformers using SMILES and Graph representations

I was wondering if either of SMILES or graph representations (in their vanilla form) can distinguish between two conformers of the same molecule. Can this be enhanced by adding additional metadata on ...
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1 vote
1 answer
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How to convert Excel comments to ChemDraw .cdx?

Not sure whether this might be a Superuser or StackOverflow question... but I hope some Chemist can help me with this. I have an Excel table with cells which contain comments "by Cambridge Soft&...
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2 votes
2 answers
159 views

How to interpret BRICS fragments

I have a molecule with a SMILES string as given below. smi='c1ccccc1OCCOC(=O)CC' I want to obtain BRICS based fragments which I did as follows. ...
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5 votes
1 answer
324 views

Converting SMILES string into valid sub-strings

I have a SMILES string as follows. smi= 'CCOC(=O)C1=C(COCCN)NC(C)=C(C(=O)OC)C1c1ccccc1Cl' Is there anyway that I convert this SMILES string into valid sub-strings ...
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1 vote
1 answer
35 views

Why should duplicates compounds be removed from compound libraries before screening/activity prediction?

This is one of the first steps to be done while analysing chemical data or applying training models to predict chemical activity. However, I am unclear as to why is this done. Doe sit have a major ...
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4 votes
2 answers
2k views

How to convert an XYZ file to Z-matrix?

I would like to generate a Z-matrix from the following XYZ file (C2H6dimer.xyz): ...
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-1 votes
2 answers
456 views

How to compare three or more molecular structures? [closed]

Let's say you have three or more different geometry files (xyz) for the same structure and you want to compare them. What would be best way for that?
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2 votes
0 answers
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On drug-like criteria and QM9 dataset

According to the book Machine Learning Meets Quantum Physics QM9 is built up from $\sim 134 \mathrm{k}$ drug-like molecules with up to nine heavy atoms (C, N, O, or F). I'm assuming that drug-like ...
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