5
votes
Mapping drug names to ATC codes
DrugBank seems to have a tool to map ATC codes to drug names and DrugBank IDs.
A quick look in the XSD schema on the release page suggests the complete database includes ATC codes for drugs, you ...
- 153
5
votes
Mapping drug names to ATC codes
The CART tool let's you upload a set of names and map them (optionally in a fuzzy way) to STITCH 4 identifiers, and then use those to map to ATC codes (using the chemicals sources download file). It's ...
- 218
3
votes
Accepted
Genomic coordinates of predicted binding pocket
It turns out there is a tool that does this beautifully. I used the proteinToGenome function from the ensembldb package.
The code looks like this:
...
- 841
3
votes
Accepted
What's a good ontology for drug names?
Since this question's been asked there's been a (what looks like a first useful?) release of Drug Ontology DRON. Perhaps worth checking again?
- 261
3
votes
How to find GEO data sets using Drug Bank ID and bioDBnet
You could take a look at the rentrez package for R. You can use the entrez_search function to get the GEO IDs for the studies ...
- 131
2
votes
Drug with as many targets as possible through a system biology graph?
I don't know any python (or R package) to do this), but this is how I would do it based on these matrices:
Do a multidimensional scaling (MDS) plot of the target_similarity matrix. Explore the ...
- 4,693
2
votes
How to find GEO data sets using Drug Bank ID and bioDBnet
One of the problems I've found with GEO and even ArrayExpress is that it seems like there are tons of false positives that come up in the search. Additionally, there may be a ton of results that you ...
- 524
2
votes
Where can I find gene expression data on one of the cell lines in NCI-60?
Cosmic Cell Lines Project provides gene expression data for 1000+ cell lines (including NCI-60 panel together with NCI-H23 cell line). For each gene in a cell line, you can get Z-score and over/under-...
- 56
2
votes
Where can I find gene expression data on one of the cell lines in NCI-60?
CellMiner portal has plenty of data about NCI-60 cell lines, inclusive microarray gene-expression.
Also, NCI-60 is a subset of the ~1000 cell lines covered by the GDSC project for which you have ...
- 183
2
votes
Accepted
Why do molecular generation models maximize “penalized logP” as a measure of drug-likeliness?
A positive logP is good (hydrophobic), but high results in ADMET problems (cytochromes break overly hydrophobic compounds) and aggregation (gunk, tar, crud are words happily thrown around). However, ...
- 4,234
1
vote
Gene rank scores from LINCS database: Evangelista et al. 2022
Summary answer
Although I'm unhappy about how the paper is written and possibly the methodology, the following sentence is likely (almost certainly) to be the answer.
The coefficient (aka weight) is ...
M__♦
- 11.9k
1
vote
Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
Yes it's easy you load everything into a dataframe, so each variable is one column and perform supervised machine learning. That will solve all questions.
Hypothesis 1 The target is 'pre' 'post' if ...
M__♦
- 11.9k
1
vote
Accepted
How to create drug synergy plot?
To get you started. Complex editing in matplotlib isn't intuitive.
...
M__♦
- 11.9k
1
vote
Help me in understanding the PDB file
well wasnt able to figure out how to make openapigenerator work with rcsb pdb ModelServer https://models.rcsb.org/, I ended up with this code
copying the webserver manual input results for ligands:
<...
- 961
1
vote
Why do molecular generation models maximize “penalized logP” as a measure of drug-likeliness?
You were trapped by arXiv versioning convention that shows you the latest version of the preprint as default. It seems that this experiment was removed from the final publication.
If you have a look ...
- 111
1
vote
Finding drugs based on gene expression data
It would be great if you can provide more information about the gene expression data set. If you have response to single drug, the general approach is to find the deferentially expressed genes with ...
- 11
1
vote
Genomic coordinates of predicted binding pocket
That PDB page includes a publication reference and abstract, containing the following text:
Mammalian CYP450s recognize and metabolize diverse xenobiotics such as
drug molecules, environmental ...
- 13.8k
1
vote
Finding new drug-protein targets/interactions using a known one as base
If you have information on which part of the protein are interacting, and its sequence, you can search for homologous or similar sequences in other proteins. This would give you a list of potential ...
- 203
1
vote
How are PDO and PDX used in computational and predicative models for tumour biology?
Potential pitfall!
I'm not sure about predictive models, but you need to be aware of a potential pitfall in blindly aligning PDX or PDO based sequencing data without first removing contaminating host ...
- 1,059
Only top scored, non community-wiki answers of a minimum length are eligible