VI-SEEM REG LS: VI-SEEM e-Infrastructure services, Molecular Dynamics Simulations of Biomolecules and Computer-Aided Drug Design

from to (Europe/Belgrade)
at Belgrade ( Room 300 )
Pregrevica 118, 11080 Belgrade, Serbia
Description

Objective: This interactive course will introduce participants to VI-SEEM e-Infrastructure services, and then focus on the principles and applications of biomolecular modeling, and pinpoint how biomolecular problems, such as drug design, are being currently addressed by computational techniques.

Aims:

  1. Introduce VI-SEEM data and computational services, and their access methods.
  2. Hands-on training in classical Molecular Dynamics (MD) simulations by examining the protein lysozyme of the NAMD program. Introduction to GROMACS.
  3. Computer-aided drug design with Schrodinger Suite and ChemBioServer. An introduction to virtual screening for computer-aided drug design and application with the Schrodinger Suite software. The generated virtual screening results are then post-processed (filtered) for toxicity, chemical similarity and validity of docking pose using the ChemBioServer software (http://bioserver-3.bioacademy.gr/Bioserver/ChemBioServer/)
Material:
Computer-Aided Drug Design unknown type file NAMD training material unknown type file pdf file PARADOX-IV NAMD, VMD, and GROMACS link Slides unknown type filedown arrow Training Evaluation Form link Training Event Summary Report word file VMD training material word file summary locked word file
Host institution support Email: slavnic@ipb.ac.rs Telephone: +381 11 3713177
Go to day
  • Wednesday, 19 October 2016
    • 09:00 - 09:15 Welcome: VI-SEEM Virtual Research Environment and Services
      start of training event
      Convener: Dr. Antun Balaž (Institute of Physics Belgrade)
      Material: slides powerpoint file
    • 09:15 - 10:00 HPC usage and software packages
      Convener: Vladimir Slavnić (Institute of Physics Belgrade)
      Material: slides powerpoint file
    • 10:00 - 10:30 VI-SEEM Source Code Repository
      Convener: Petar Jovanović (Institute of Physics Belgrade, Serbia)
      Material: slides pdf file
    • 10:30 - 11:00 Coffee break
    • 11:00 - 11:30 VI-SEEM Data Repository
      Convener: Vladimir Slavnić (Institute of Physics Belgrade, Serbia)
      Material: slides powerpoint file
    • 11:30 - 12:30 VI-SEEM Staging and Archiving
      Convener: Petar Jovanović (Institute of Physics Belgrade, Serbia)
      Material: slides pdf file
    • 12:30 - 13:30 Lunch
    • 13:30 - 14:00 Related LS e-Infrastructure initiatives: BioExcel
      Convener: Rossen Apostolov (KTH)
    • 14:00 - 14:30 Introduction to VI-SEEM LS services, workflows, applications, and data sets
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
      Material: slides powerpoint file pdf file
    • 14:30 - 15:00 Coffee break
    • 15:00 - 16:30 Introduction to Computer Modeling of Biomolecules
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 16:30 - 18:00 Hands-on training: Visualization of Biomolecules using VMD
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 20:00 - 21:00 VI-SEEM Social Dinner ( Dva Jelena Skadarlija )
  • Thursday, 20 October 2016
    • 09:30 - 11:00 Hands-on training: Molecular Dynamics Simulations of the lysozyme protein using NAMD: 1. Minimization
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 11:00 - 11:15 Coffee break
    • 11:15 - 13:00 Hands-on training: Molecular Dynamics Simulations using NAMD: 2. Equilibration
      Convener: Cournia Zoe (Biomedical Research Foundation Academy Of Athens, Greece)
    • 13:00 - 14:00 Lunch
    • 14:00 - 14:30 Example of successful VI-SEEM application of Molecular Dynamics Simulations: Polyethyleneimine loaded inverse SDS micelle in pentanol/toluene media
      Convener: Hrachya Astsatryan (Institute for Informatics and Automation Problems, National Academy of Sciences, Armenia)
    • 14:30 - 17:00 Hands-on training: Molecular Dynamics Simulations using NAMD: 3. Dynamics
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
  • Friday, 21 October 2016
    • 09:30 - 11:00 Hands-on training: Molecular Dynamics Simulations using NAMD: 4. Analyzing MD trajectories
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 11:00 - 12:00 Introduction to GROMACS
      Convener: Cournia Zoe (Biomedical Research Foundation Academy Of Athens, Greece)
    • 12:00 - 13:00 Introduction to Computer-aided drug design: Principles and applications of the method using the Schrodinger Suite and the ChemBioServer
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 13:00 - 14:00 Lunch
    • 14:00 - 15:30 Hands-on training: Computer-Aided Drug Design
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)