YASARA

A comprehensive molecular modeling and simulation package with an intuitive user interface.

Overview

YASARA is a powerful molecular modeling and simulation package that combines molecular visualization, structure prediction, and molecular dynamics simulation capabilities in a user-friendly interface. It is particularly well-suited for both beginners and advanced users in structural biology and drug design.

Features

Interactive molecular visualization
Structure prediction and modeling
Molecular dynamics simulation
Docking and virtual screening
Sequence alignment and analysis
Automated structure refinement
Scripting capabilities

Installation

Requirements

Windows, macOS, or Linux
OpenGL 3.3+ compatible graphics card
4GB+ RAM
2GB+ disk space

Installation Steps

Download YASARA:

wget https://www.yasara.org/downloads/yasara.tar.gz
tar xzf yasara.tar.gz

Run the installer:
```
cd yasara
./install.sh
```

Basic Usage

Example Script

# Load a protein structure
LoadPDB "1crn.pdb"

# Perform energy minimization
Minimize

# Run molecular dynamics
MD

# Save the results
SavePDB "minimized.pdb"

Advanced Topics

Structure Prediction

YASARA offers various structure prediction methods:

Homology modeling
Loop modeling
Side chain prediction
Structure refinement

Molecular Docking

Protein-ligand docking
Protein-protein docking
Virtual screening
Binding energy calculation

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