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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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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360 views

OpenBabel: how to get correct SMILES from Gaussian output?

I would like to get the molecular structure as SMILES from Gaussian output files. OpenBabel seems to be the tool made for such tasks. However, the structure is not always correct. One example: ...
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163 views

What is the dataset with the largest number of molecules?

In computational chemistry we often apply techniques to all molecules of a "dataset". Recently it was asked which dataset contains the largest molecules, and a user accidentally misinterpreted this ...
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366 views

Pseudo 3D skeletal structure style which emphasizes geometry

If one searches and navigates to a wiki page for, say, dichlorodifluoromethane one sees the 2D skeletal structure of the compound as below This representation appears to be of a particular style that ...
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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 ...
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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 ...
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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 ...
4
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35 views

Validity of graph-based molecular representation in ML

I was reading about molecular graph based generative models, which attempt to generate new molecules by training on a subset of a molecular dataset, such as QM9. In these works, there are 2 types of ...
3
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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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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....
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48 views

Bioinformatics tools for predicting synthetic reaction for identified drugs?

We are aware of many bioinformatics open source tools like AUTODOCK, Smina for drug discovery through structure based virtual screening. I was wondering if there are validated bioinformatics tools ...
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421 views

Open Babel: conversion to SMILES. How to delete H?

OpenBabel is a convenient converter between different chemical formats. If I convert to SMILES, however, although I checked the option "Delete hydrogens (make implicit)". I still have ...
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86 views

Matchmol for substructure determination

I'm using Checkmol/Matchmol for substructure determination and retrieval, and I'm having problems determining whether a given molecule is the substructure of another molecule when they have the same ...
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101 views

In QSAR, what is the simplest (but most powerful) way to create an applicability domain model?

QSAR means Quantitative Structure Activity Relationship. An applicability domain model is a model that tells you how far you are from the domain where your model was trained. I.e. it is a kind of map ...
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229 views

How to get the SMILES from structure without software?

Usually I use online programs and structure drawing tools to find the SMILES of a compound. How to find the SMILES without software? Where to find resources to learn it?
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164 views

Obtaining chemical graph complexity index from SMILES or InChl

I wonder if anyone knows a readily available way to obtain some chemical graph complexity index (like the J index) from the SMILES or InChl representations?I'm looking for some existing implementation,...
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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 ...
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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. <...
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32 views

Order of features in chemical descriptors

ECFP are small-molecule descriptors, which are usually represented as a bit vector. I wonder if order of elements of this vector matters, in other words, if this vector encodes any positional ...
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110 views

Non central chirality in cheminformatics?

What are compact cheminformatics structural representations that allow to deal correctly with axial chirality, such as in binaphthyl compounds or metal complexes?
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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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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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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 ...
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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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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 ...
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23 views

How to calculate Wiener index for aromatic and cyclic organic compounds?

I have been searching for literature on calculating the Wiener index for aromatic and cyclic organic compounds. For acyclic aliphatic compounds the methodology is straightforward obtained from ...
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134 views

Valency of each atom in a molecule with python

Consider ethanol, where each carbon atom has a valency of 4 and oxygen a valency of -2. I would like to determine these values for many compounds given their SMILES or InChI keys. (For the purpose of ...
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37 views

Online list of water of crystallisation?

I was extremely happy to recently receive a copy of the Nuffield Revised Book of Data but was somewhat disappointed to find that it did not list data on the water of crystallisation for various ...
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114 views

Conversion of standard InChI to InChI with fixed-hydrogen-layer

I am trying to convert a standard InChI string to a non-standard InChI string with fixed-hydrogen-layer: Standard InChI for Uracil: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) Desired ...
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102 views

How to store molecule data using SMILES when building a toy chemistry model

I'm currently building a toy chemistry model based around Gillespie's algorithm. Starting from a food set of {H,O,N,C} I let my system evolve, I have been storing my molecules as strings in SMILES ...
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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 ...
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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 ...