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Questions tagged [drugs]

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1answer
47 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
65 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
52 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
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1answer
28 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
47 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
172 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 ...
3
votes
1answer
154 views

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

There are 2 new wet methods: Patient-derived models: Patient Derived Xenograft (PDX) and Patient Derived Organoids (PDO) to reflect tumor biology. Are there any databases/resources/computational ...
6
votes
3answers
97 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
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2answers
298 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 ...