Molecular docking is a crucial method in computational drug discovery, allowing researchers to predict the binding of small molecules (ligands) to their target proteins. AutoDock Vina is a popular tool for this purpose, producing docked poses as output files. However, when these output files are loaded into visualization tools like DS Visualizer (Discovery Studio Visualizer), users sometimes encounter issues such as broken structures or scattered fragments. In this article, we provide a new Python script to solve this issue.

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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).

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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).

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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.

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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.

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High-throughput virtual screening (HTVS) is a pivotal technique in drug discovery that screens extensive libraries of compounds to find potential drug candidates. One of the essential tasks in HTVS is to ensure that ligands are binding within the protein’s binding pocket. This task can be particularly challenging when dealing with thousands of docking results. To address this challenge, we present a Python script that automates the analysis of molecular docking results generated by AutoDock Vina [1] using PyMOL [2]. This script calculates the center of mass (COM) for each docked pose, compares it with a reference ligand’s COM, and identifies poses that bind within a specified threshold distance. This process is crucial in mass docking scenarios where confirming ligand binding within the pocket is necessary. (more…)

Copying and renaming files from one destination to another is easily accomplished by the cp command in Linux. However, it becomes more complex when we want to copy and rename all files in the same directory while assigning a serial number to each copy. In this article, we provide a shell script to copy and rename files present in a directory, adding a unique serial number to each copy.

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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).

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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.

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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].

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Protein structure file (PSF) contains topology information and is required for molecular dynamics (MD) simulation in NAMD [1] and VMD [2]. In this tutorial, we will generate a PSF file of a simple protein using NAMD and VMD.

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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.

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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.

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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.

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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).

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DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

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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).

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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.

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A new study has revealed new forms of proteins that have never been seen before along with unexpected connections. Last year, Google DeepMind predicted the structure of all known proteins from organisms using AlphaFold [1].

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In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.

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