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...
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...
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...
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:...
In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.
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...
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.
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...
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...
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...
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.
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...
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...
Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.
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....
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.
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...
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,...
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