Tools
Converting smiles into 3D structures using openbabel.
Openbabel is used to inter-convert many file formats [1]. It is available for Linux, Windows, and MAC operating systems. In this article, we will learn how to generate 3D structures of compounds present in the form of smiles on Ubuntu as well as on Windows.
On Ubuntu
You can download the openbabel software on Ubuntu from the repository as shown below:
$ sudo apt-get install openbabel
.
Save your downloaded smiles into smiles format (.smi), for example, ‘smiles.smi’. This is our input file. To generate 3D structures of these smiles into SDF format, type the following commands:
$ obabel -i smi smiles.smi -o sdf -O out.sdf -m -h --gen3d
Here, -m
is used to split the output into multiple files. It is used in batch conversion, where you have multiple smiles in a single file (as described in this article) and you want individual files as output. -h
adds hydrogens.
--gen3d
is used to generate 3D coordinates for the structure.
Similarly, they can be converted into pdb as well as shown below:
$ obabel -i smi smiles.smi -o pdb -O out.pdb -m -h --gen3d
You can also convert files other than smiles. For example, pdb, mol, SDF, and so on. Just change the input-ID and input filename along with the output-ID and output filename according to your requirements.
For more options, type $ obabel -H
.
On Windows
On Windows, you can download the binary file from here. You can use the GUI of openbabel as follows.
- Open the openbabel after installation.
- Upload your input file and specify the input format from the dropdown.
- Select options appropriate to your needs such as ‘Generate 3d’, ‘Output multiple conformers separately’, and so on.
- Select the output format and output file location.
- Click ‘Convert’.
You can input smiles or any other format using the editor given on the left side of GUI and obtain output without saving into any files.
References
- O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of cheminformatics, 3(1), 33.
Docking
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.
Docking
How to install the DockingPie plugin on PyMOL?
DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).
Structural Bioinformatics
How to predict binding pocket/site using CASTp server?
The CASTp server allows you to predict the binding sites in a protein [1]. In this article, we will predict binding sites in a protein using the same.
Software
Video Tutorial: Calculating binding pocket volume using PyVol plugin.
This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].
Software
How to generate topology from SMILES for MD Simulation?
If you need to generate the topology of molecules using their SMILES, a simple Python script is available.
Software
[Tutorial] Installing jdock on Ubuntu (Linux).
jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).
Software
How to install GMXPBSA on Ubuntu (Linux)?
GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).
Docking
[Tutorial] Installing Pyrx on Windows.
Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)
MD Simulation
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
Software
Installing Autodock4 on MacOS.
Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.
Docking
How to install Autodock4 on Ubuntu?
Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.
Software
DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.
Software
Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
RNA-seq analysis
Pathonoia- A new tool to detect pathogens in RNA-seq data.
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].
Software
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)
Software
How to calculate binding pocket volume using PyVol plugin in PyMol?
Software
How to generate electron density map using Pymol?
Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
Software
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)
Tips & Tricks
How to download FASTA sequences from PDB for multiple structures?
In this article, we are going to download FASTA sequences for multiple structures from PDB [1]. We need to have PDB IDs only for input. (more…)
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