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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In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.

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Computational docking is not a trivial task once we avoid making some mistakes. In this section, let’s learn about some important points that we should keep in mind while performing computational docking.

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This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

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If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

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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).

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In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)

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).

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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…)

Visualizing plots of molecular dynamics simulation is easy once you have generated them. Previously, we provided a few articles on MD output analysis (check the Further Reading section). This article explains how you can easily visualize the plots generated from GROMACS output. (more…)

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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Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.

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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.

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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.

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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…)

While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article, we will learn to calculate nsteps for an MD run. (more…)

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].

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In this article. we are creating a pie chart of the docking score of five different compounds docked with the same protein. (more…)

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…)