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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1answer
71 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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0answers
22 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 ...
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1answer
69 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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0answers
24 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 ...
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1answer
35 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 ...
5
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1answer
76 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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0answers
36 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 ...
2
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2answers
81 views
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1answer
49 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: ...
5
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1answer
69 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 ...
0
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1answer
54 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 ...
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0answers
118 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 ...
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2answers
115 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 ...
2
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1answer
56 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 ...
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0answers
36 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 ...
5
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1answer
160 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 ...
3
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1answer
91 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 ...
6
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1answer
198 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 ...
6
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1answer
116 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 ...
5
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1answer
231 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 ...
4
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0answers
51 views

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 ...
12
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3answers
699 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 ...
2
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1answer
118 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 ...
6
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1answer
80 views
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0answers
126 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 ...
4
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1answer
68 views

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 ...
2
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1answer
113 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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120 views

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 ...
7
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1answer
70 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"....
8
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1answer
185 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 ...
3
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1answer
88 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 ...
3
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2answers
167 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 ...
3
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0answers
41 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 ...
3
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1answer
116 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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1answer
258 views

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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1answer
85 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. ...
5
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1answer
259 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 ...
1
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1answer
34 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 ...
4
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2answers
1k 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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2answers
281 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?
2
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0answers
64 views

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 ...
4
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2answers
509 views

SMILES string convertors

I'm new to SMILES strings, and have noticed that they're not standardised. Firstly, what is the reason for different structures of SMILES strings to represent the same compound? Why not have a ...
0
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1answer
99 views

Naming a synthetic molecule from QM9 dataset [closed]

I was trying to write a name for a synthetic molecule in QM9 dataset. The molecule is: is 3-aminooxolane-2-carbonitrile a correct name for this?
0
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0answers
61 views

Graph representation of polymer nanocomposites

Graph theory has been used as a means of representing molecules for decades. For a single molecule, a graph representation assigns a vertex for every atom in the molecule and the covalent bonds are ...
3
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0answers
154 views

Is there a Python module for calculating Ovality of a molecule?

Ovality gives a measure of how the shape of a molecule approaches a sphere (at one extreme) or a cigar shape (at the other). Ovality is described by a ratio of volume to area (see https://en.wikipedia....
4
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1answer
283 views

Openbabel is not converting Gaussian Z-matrix

I ran into an issue when OpenBabel (a great and extremely useful problem) could not convert my custom-generated Gaussian Z-matrix to XYZ format. The problem is that probably major flaw of OpenBabel ...
7
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1answer
654 views

Alternative python modules to RDKit to convert SMILES to structure

Python module RDKit is great, but it cannot be installed by pip, and therefore it is difficult to use it sometimes in a virtual environment. I am wondering that if ...
4
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0answers
48 views

Illegal valence meaning

I'm using the rdkit package to process some molecules. I noticed that when creating a molecule from a SMILES string the library does some syntactic and some semantic checks. This question regards the ...
3
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2answers
557 views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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0answers
332 views

Getting warnings during SDF to PDB conversion using obabel?

I did batch conversion of SDF to PDB for the Maybridge Screening library (containing ~50000 ligands) using obabel batch conversion tool using the following code. <...