Questions tagged [drugs]

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1answer
50 views

Finding drugs based on gene expression data

I've got a list of genes and I want to assess their association with drugs based on gene expression data sets. A comprehensive tutorial would also be helpful. Any help would be appreciated.
2
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1answer
73 views

Drug with as many targets as possible through a system biology graph?

I have 4 pandas data frames containing the following data: affinity_score1: affinity between each couple (Drug-Target) measured using tool1 affinity_score2: affinity between each couple (Drug-Target)...
2
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2answers
56 views

Genomic coordinates of predicted binding pocket

I would like to know the genomic coordinates of a proteins ligand-binding pocket. For example, on this PDB page you can see that there is xray crystallography data for how CYP2C9 interacts with two ...
1
vote
1answer
31 views

Finding new drug-protein targets/interactions using a known one as base

Given a known interaction of a molecule with some proteases (having X-rays images too) is it possible to predict interactions with other proteins either using their 3D structure or not? If anyone ...
3
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2answers
49 views

Where can I find gene expression data on one of the cell lines in NCI-60?

I'm trying to retrieve the most expressed genes from a cell line from the NCI-60, lets say cell line NCI-H23, but I'm not sure where to find the gene expression data. My main goal is to create a ...
7
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1answer
214 views

What's a good ontology for drug names?

I have ... A database with patient phenotypes in, stored as HPO terms Genetic data in whatever format I need I want ... To store drug names in a way that won't make my life difficult If it's ...
4
votes
1answer
185 views

How are PDO and PDX used in computational and predicative models for tumour biology?

There are wet methods: Patient-derived models: Patient Derived Xenograft (PDX) and Patient Derived Organoids (PDO) to reflect tumor biology. Are there any databases or computational tools that use ...
6
votes
3answers
120 views

How to find GEO data sets using Drug Bank ID and bioDBnet

I want to find all experiments in GEO that are associated with a drug (for example tolvaptan). Is there any quick and scalable way to to this? I want to query more than 100 drugs. I tried to use ...
12
votes
2answers
416 views

Mapping drug names to ATC codes

I'm interested working with the medication information provided by the UK Biobank. In order to get these into a usable form I would like to map them to ATC codes. Since many of the drugs listed in ...