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Cheminformatics

Installing CDK (Chemistry Development Kit) on Ubuntu (Linux)

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Installing cdk on Ubuntu

CDK stands for chemistry development kit [1]. This is an open source kit for cheminformatics consisting of modular JAVA libraries. In this article, we will install CDK on Ubuntu.

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing prerequisites

You need to install the following packages to run CDK on your system. Paste the following command in the terminal.

$ sudo apt-get install -y maven

$ sudo apt-get install -y default-jdk

Downloading CDK

At first, change to the directory where you want to download the software. Let’s say ‘Downloads‘.

$ cd Downloads/

You can either manually download the latest version of the CDK from here or use the following command.

$ wget https://github.com/cdk/cdk/archive/refs/tags/cdk-2.5.tar.gz

It will take a moment to finish downloading.

Installing CDK

Extract the downloaded package.

$ tar xvzf cdk-2.5.tar.gz

A new directory would have been created namely, cdk-cdk-2.5. Change to this new directory to install.

$ cd cdk-cdk-2.5/

Now install using the following command.

$ mvn install

It will be finished in a few moments.


References

  1. Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., & Willighagen, E. (2003). The Chemistry Development Kit (CDK): An open-source Java library for chemo-and bioinformatics. Journal of chemical information and computer sciences43(2), 493-500.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Bioinformatics Programming

How to obtain ligand structures in PDB format from PDB ligand IDs?

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How to obtain ligand structures in PDB format from PDB ligand IDs?

Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this article, we are downloading PDB ligand structures from their corresponding IDs. (more…)

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Cheminformatics

cheML.io: ML-generated molecules database

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cheML.io: ML-generated database of molecules

Due to the advancement of machine learning (ML) methods, we can find increasing applications of them in the field of bioinformatics as well. ML is being utilized in making personalized medicines, similarity searches in DNA and protein sequences, phylogenetics by mapping selected species on phylogenetic trees, gene and protein function annotation, generating chemical compounds, and so on. In this article, we will discuss an online database of ML-generated molecules known as cheML.io [1].

(more…)

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Bioinformatics Programming

How to obtain SMILES of ligands using PDB ligand IDs?

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How to obtain SMILES of ligands using PDB ligand IDs?

Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)

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