MM/GB(P)SA free energy calculations using various programs
Konu özeti
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MM/GB(P)SA free energy calculations using various programs
Skill Level: Advanced
Language: English
Workload: 2 hours total
Topic: Computational Biophysics
Overview: The course will show how to use tools for calculating binding free energy on the simulation trajectories produced by popular Molecular Dynamics Simulation engines.
Course Description: This online course aims at demonstrating how to perform MM/GB(P)SA calculations on HPC platforms. These calculations are one of the mostly performed calculations in drug discovery studies. Typically, these are used to estimate binding affinities of ligand molecules to target biomolecules (ex: receptor proteins).
Course Contents:
Lesson1: MM/PBSA calculation using CaFE (NAMD)
Lesson2: MM/GB(P)SA Using AmberTools (Amber)
Lesson3: MM/PBSA calculation using gmx_MMPSA (Gromacs)
Who Should Enroll: Individuals interested in performing MM/GB(P)SAcalculations on HPC platforms.
Prerequisites:
Basic knowledge in Molecular Dynamics simulations
Familiarity with Linux/Unix operating systems
Basic Knowledge in slurm job submission etc on a HPC
General knowledge in MM/GB(P)SA calculations
Tools, libraries, frameworks used: Python, VMD, NAMD, AmberTools, Gromacs
Learning Objectives: Installing popular MM/GB(P)SA tools on HPC and being able to perform these energy calculations on HPC systems
About the instructor(s): https://akademi.itu.edu.tr/tr/badays/Sefer-Baday/