Simulations in
Discovery Studio - Training

Overview -
Simulations in Discovery Studio Training

The course will provide an overview of molecule mechanics, energy minimization, molecular dynamics, and analysis tools and protocols available in Discovery Studio

Audience - Simulations in Discovery Studio Training

This training is ideal for customers who use or plan to use Discovery Studio Biopolymer, Discovery Studio CHARMm, and Discovery Studio Analysis.

On completion of the workshop the user will have covered:

• Build and visualize proteins, peptides, and small molecules
• Prepare a PDB file for a molecular mechanics simulation
• Perform an energy minimization cascade using CHARMm
• Prepare a molecular dynamics simulation and analyze the results
• Apply constraints to a molecular system
• Include explicit or implicit solvation effects in molecular mechanics simulations
• Perform manual and automatic force field potential typing and charge assignment
• Perform analysis of molecular trajectories using tools and protocols
• Perform CHARMm-based docking using CDOCKER
• Evaluate intermolecular interactions and determine binding energies
• Perform electrostatic potential calculations using DelPhi
  

Sample Agenda

Web-based Course

Day 1:

• 15 minutes Welcome and Administration Announcements
• 30 minutes Overview
• Break
• 1 hour System Preparation and Force Fields
• Break
• 30 minutes Energy Minimization and Electrostatics
• 30 minutes Solvation
  

Day 2:

• 10 minutes Review
• 50 minutes Molecular Dynamics and Constraints
• Break
• 1 hour Analyzing Structures and Properties
• Break
• 45 minutes CHARMm-Based Docking and Scoring

On-site Course

Day 1:

• 9:00 – 9:15: Welcome and Administration Announcements
• 9:15 – 9:45: Overview
• 9:45 – 10:00: Break
• 10:00 – 11:00: System Preparation and Force Fields: Lecture
• 11:00 – 12:00: System Preparation and Force Fields: Exercises
• 12:00 – 1:00: Lunch
• 1:00 – 1:45: Energy Minimization and Electrostatics: Lecture
• 1:45 – 2:45: Energy Minimization and Electrostatics: Exercises
• 2:45 – 3:00: Break
• 3:00 – 3:45: Solvation: Lectures
• 3:45 – 5:00: Solvation: Exercises
  

Day 2:

• 9:00 – 9:15: Review
• 9:15 – 10:15: Molecular Dynamics and Constraints: Lectures
• 10:15 – 10:30: Break
• 10:30 – 12:00: Molecular Dynamics and Constraints: Exercises
• 12:00 – 1:00: Lunch
• 1:00 – 2:00: Analyzing Structures and Properties: Lectures
• 2:00 – 2:15: Break
• 2:15 – 3:00: Analyzing Structures and Properties: Exercises
• 3:00 – 3:45: CHARMm-Based Docking and Scoring: Lectures
• 3:45 – 5:00: CHARMm-Based Docking and Scoring: Exercise