Welcome to Rocha’s Lab Computational Biochemistry Unit!

Departamento de Bioquímica e Biologia Molecular (UFSM) Programas de Pós-Graduação em Ciências Biológicas: Bioquímica Toxicológica - PPGBTox Programa de Pós-Graduação em Educação em Ciências: Química da Vida e Saúde - PPGECQVS Centro de Ciências Naturais e Exatas - CCNE 97105-900 Santa Maria RS Brasil

Computational Biochemistry is a field of biochemistry that uses computational technologies in biochemical research.

Check out the Usage section for further information, including how to Installation the project.

Note

This project is under active development.

Contents

• Rigid Docking
  • Installation
  • Example 1: Joao Vitor
• Flexible Docking
  • Installation
  • Creating recipes
• Protein-protein Docking
  • Installation
  • Example 1: Tamie Duarte
  • Creating recipes
• Molecular Dynamics Simulation
  • Installation
  • Protocol
  • Preparation of input files:
  • Using Antechamber:
  • Examining force field parameters with parmchk2
  • Setting up the simulation:
  • Running the simulation:
  • Load the trajectory file into Amber.
  • Example 1
• Density Functional Theory
  • Installation
  • Creating recipes