BioDiscovery Group, India in collaboration with Biotech Labs, Egypt will conduct 2 day training in Molecular Simulations & Dynamics entitled "Practical approach in Molecular Simulations & Dynamics | Insights of Computational Biophysics"
Molecular dynamics simulations are powerful computational techniques meant to study structure, function and interactions of biomolecules at the atomic level such as membrane proteins, ion channels and nucleic acids. In addition, molecular dynamics simulations are important for studying and validation protein structure and protein-ligand interactions as part of the drug discovery process.
The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level.
This workshop will highlight this powerful computational technique and provide hands on practical experience on this technique. After lecture and discussions, participants will learn how to model a biological molecule such as a particular protein, solvate the protein, run minimization, equilibration and protein simulation and analyze the simulations.
Making a protein structure file
Solvating the protein in a water box
Adding ions to the solvated protein
NAMD configuration file
Minimization and equilibration
Simulations parameters and running the simulations
Analysis of the simulations
Examples of case studies from the literature with emphasis on protein-ligand interactions, protein dynamics and function.
VMD (Visual Molecular Dynamics)- VMD is a free software designed for modeling and visualization of biomolecules such as proteins, nucleic acids, biomembranes, etc. VMD can read and display standard Protein Data Bank (PDB). VMD can also analyze the trajectory of a molecular dynamics (MD) simulation. Specifically, VMD can act as a graphical front end for an external MD program, NAMD, by displaying and animating a molecule undergoing simulation.
NAMD (Scalable Molecular Dynamics)- NAMD is a free code for the simulation of large biomolecular systems. NAMD uses the molecular visualization program, VMD, for simulation set up and trajectory analysis.
Text editor (WordPad or Notepad for windows users, emacs and vi for Mac OS X and Linux users)
Plotting program (Excel or Scilab for Windows users, gnuplot and xmgrace for Mac OS X and Linux users)
BRING YOUR OWN LAPTOPS FOR SOFTWARE & TRAINING
Lunch & Refreshment
The workshop is designed for graduate and Master students as well as PhD and Postdoctoral researchers. It is also helpful for scientists and company professionals from life sciences background especially in computational and/or biophysical fields who want to enhance their skills of computational biophysics skills.
For bank transfer kindly contact-
Account name: Biotech
Account number: 196-1-7861
Bank: Banque Misr
Please visit us at, 399 Ramses St., In front of El Demerdash hospital, Abasia, Egypt from 09:00 am to 09:00 pm
399 Ramses St., In front of El Demerdash hospital, Abasia, Egypt