![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1.jpg)
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
DockingPie is a PyMOL plugin to perform computational docking within PyMOL .…
How to install the DockingPie plugin on PyMOL?
DockingPie is a plugin of PyMOL made to fulfill the purpose of…
How to predict binding pocket/site using CASTp server?
The CASTp server allows you to predict the binding sites in a…
Proteins shape analyses reveal novel forms and connections.
A new study has revealed new forms of proteins that have never…
Energy minimization and equilibration of simple protein using NAMD & VMD.
In this tutorial, we will perform energy minimization and equilibration of a…
Generating topology of molecule for AMBER forcefield for GROMACS.
In this article, we will generate the topology of a small molecule…
Common mistakes made during computational docking.
Computational docking is not a trivial task once we avoid making some…
Video Tutorial: Calculating binding pocket volume using PyVol plugin.
This is a video tutorial for calculating binding pocket volume using the…
How to generate topology from SMILES for MD Simulation?
If you need to generate the topology of molecules using their SMILES,…
![[Tutorial] Installing jdock on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/05/09092952/jdock.jpg)
[Tutorial] Installing jdock on Ubuntu (Linux).
jdock is an extended version of idock . It has the same…
How to upgrade cmake on Ubuntu (Linux)?
In bioinformatics, cmake is used to install multiple software including GROMACS, jdock,…
How to install GMXPBSA on Ubuntu (Linux)?
GMXPBSA is a tool to calculate binding free energy . It is…
![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
[Tutorial] Installing Pyrx on Windows.
Pyrx is another virtual screening software that also offers to perform docking…
How to visualize output plots of MD simulation (GROMACS)?
Visualizing plots of molecular dynamics simulation is easy once you have generated…
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS with GPU can be trivial. Previously, we have provided a…
Installing Autodock4 on MacOS.
Previously, we installed the Autodock suite on Ubuntu. Visit this article for…
How to install Autodock4 on Ubuntu?
Autodock suite is used for docking small molecules . Recently, Autodock-GPU is…
DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing,…
Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there…
How to calculate number of steps (nsteps) for MD simulation run?
While doing molecular dynamics (MD) simulation, it can be difficult to calculate…