Tools
How to build molecules in Pymol?
Pymol [1] has many functions that you keep finding on exploration. In this article, we will explain how to draw molecules in Pymol.
Assuming you have Pymol installed on your system. If not, then read this article to install Pymol on Ubuntu.
Getting Started
- Open Pymol on Ubuntu either by typing
pymolon the terminal and on Windows by double-clicking the app. - Go to the top-right corner where you can see some options such as Reset, Zoom, Draw, etc. In the last row, you will see an option namely, Builder. Click on it.
- After clicking on it, you will see a small window consisting of some chemical structures, atoms, and bonds.
Building simple molecule
- Choose whatever chemical structure you want, for example, benzene, carbon, oxygen, and so on.
- Click on a structure, for instance, benzene.
- Go to the right-hand side panel. You will see three tabs: (i) Create As a New Object, (ii) Combine w/ Existing Object, and (iii) Done.
- Click on the first tab, i.e.,
Create As a New Object. - Now click on the blank space on the Pymol screen. You will see a benzene structure.
- Now add other atoms or bonds as per your requirement.
- You can undo any step by pressing Ctrl+Z, create bonds, clear up the whole screen, add charge, set up a cycle bond (for that click on
Cyclewritten in front of ‘Bonds:’ in the builder window) and so on.
Similarly, you can add some amino acids to the structure.
- Repeat the above steps and then switch to the ‘Protein’ tab on the Builder window.
- Click on the amino acids you wish to add to the structure.
- After finishing the structure, you can save it as a PDB file.
Saving the molecule in PDB format
- Go to
File --> Export Molecule --> PDB Options --> Write CONECT records for all bonds --> Save. - You can select other formats such as MOL2, Maestro, XYZ, and so on.
References
- The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
DS Visualizer is a comprehensive, free molecular modeling and visualization tool designed by BIOVIA, part of Dassault Systèmes [1]. It enables researchers to visualize and analyze complex chemical and biological data, including molecular structures, sequences, and simulations.DS Visualizer’s user-friendly interface supports various file formats and provides powerful tools for molecular editing, docking, and structure analysis. In this article, we are installing DS Visualizer on Ubuntu (Linux).
![[Tutorial] Installing HTSlib on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2024/08/03204655/htslib.jpg)
HTSlib is an open-source C library designed for handling high-throughput sequencing (HTS) data [1]. It provides the underlying functionality for manipulating various file formats commonly used in genomics, such as SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map), CRAM (Compressed Reference-oriented Alignment Map), and VCF (Variant Call Format). In this article, we are installing on Ubuntu (Linux).
Molecular Dynamics (MD) simulation analysis involves interpreting the vast amounts of data generated during the simulation of molecular systems. These analyses are necessary to study the physical movements of atoms and molecules, the stability of molecular conformations, reaction mechanisms, and thermodynamic properties, among other aspects. In this article, we will give a brief overview of some widely used MD simulation analysis tools.
ProteStAr is a bioinformatics tool to compress protein structure files [1]. It compresses PDB/CIF files and supplementary PAE files. The compression is lossless. However, users are allowed to generate the lossy compression of files. In this article, we are installing ProteStar on Ubuntu.
Understanding the relationship between genes and proteins is crucial for elucidating biological processes, and disease mechanisms, and developing targeted therapies. A new tool developed by Yang et. al., [1], provides a better solution to map annotated positions and variants to protein structures automatically. 3Dmapper is a stand-alone tool based on R and Python programming languages that map annotated genomic variants or positions to protein structures [1]. In this article, we will install 3Dmapper on Ubuntu (Linux).
CMake is a widely used cross-platform build system that automates the process of compiling and linking software projects. In bioinformatics, CMake can be utilized to manage the build process of software tools and pipelines used for data analysis, algorithm implementation, and other computational tasks. However, managing the versions of CMake or upgrading it on Ubuntu (Linux) can be a trivial task for beginners. In this article, we provide methods for installing and upgrading CMake on Ubuntu.
Bioinformatics Programming
Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.
In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It is difficult to understand and plot a meaningful FEL and then extract the time frames at which the plot shows minima. In this article, we introduce a new Python package (Free_Energy_Landscape-MD) to generate an FEL based on principal component analysis (PCA) from MD simulation done by GROMACS [1].
Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.
Bioinformatics Programming
vs_interaction_analysis.py: Python script to perform post-virtual screening analysis
Analyzing the results of virtual screening (VS) performed with Autodock Vina [1] can be challenging when done manually. In earlier instances, we supplied two scripts, namely vs_analysis.py [2,3] and vs_analysis_compounds.py [4]. This time, we have developed a new Python script to simplify the analysis of VS results.
Interactive Genome Viewer (IGV) is an interactive tool to visualize genomic data [1]. In this article, we are installing IGV and tools on Ubuntu desktop.
![[Tutorial] Installing VIAMD on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/12/01184130/viamd.jpg)
Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing it on Ubuntu (Linux).
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1.jpg)
DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.
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).
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.
This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].
If you need to generate the topology of molecules using their SMILES, a simple Python script is available.
![[Tutorial] Installing jdock on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/05/09092952/jdock.jpg)
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).
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).
![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
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.
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