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

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Room 300 (Belgrade)

Room 300

Belgrade

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/)
Computer-Aided Drug Design
NAMD training material
PARADOX-IV NAMD, VMD, and GROMACS
Slides
summary
Training Evaluation Form
Training Event Summary Report
VMD training material
Participants
  • Bojana Koteska
  • Djordje Francuski
  • Evdokiya Salamanova
  • Gergana Gocheva
  • Gjoshe Stefkov
  • Jasmina Tonic Ribarska
  • Jelena Randjelovic
  • Kleitos Sokratous
  • Luka Ilic
  • Maja Simonoska Crcarevska
  • Mihail Matenco
  • Milan Senćanski
  • Milica Radibratovic
  • Miljan Bigovic
  • Mohammad Alfraheed
  • Nikoleta Ivanova
  • Strahinja Stevanovic
  • Yevgeni Mamasakhlisov
  • Zarko Zecevic
  • Zorica Naumovska
Dušan Vudragović
  • Wednesday, 19 October
    • 09:00 → 09:15
      Welcome: VI-SEEM Virtual Research Environment and Services Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia

      start of training event

      Convener: Dr Antun Balaž (Institute of Physics Belgrade)
      slides
    • 09:15 → 10:00
      HPC usage and software packages Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Dusan Vudragovic (Institute of Physics Belgrade)
      slides
    • 10:00 → 10:30
      VI-SEEM Source Code Repository Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Petar Jovanović (Institute of Physics Belgrade, Serbia)
      slides
    • 10:30 → 11:00
      Coffee break 30m Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
    • 11:00 → 11:30
      VI-SEEM Data Repository Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Vladimir Slavnić (Institute of Physics Belgrade, Serbia)
      slides
    • 11:30 → 12:30
      VI-SEEM Staging and Archiving Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Petar Jovanović (Institute of Physics Belgrade, Serbia)
      slides
    • 12:30 → 13:30
      Lunch 1h Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
    • 14:00 → 14:30
      Introduction to VI-SEEM LS services, workflows, applications, and data sets Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
      slides
    • 14:30 → 15:00
      Coffee break Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
    • 15:00 → 16:30
      Introduction to Computer Modeling of Biomolecules Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 16:30 → 18:00
      Hands-on training: Visualization of Biomolecules using VMD Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 20:00 → 21:00
      VI-SEEM Social Dinner 1h Dva Jelena Skadarlija

      Dva Jelena Skadarlija

      Belgrade
  • Thursday, 20 October
    • 09:30 → 11:00
      Hands-on training: Molecular Dynamics Simulations of the lysozyme protein using NAMD: 1. Minimization Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 11:00 → 11:15
      Coffee break 15m Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
    • 11:15 → 13:00
      Hands-on training: Molecular Dynamics Simulations using NAMD: 2. Equilibration Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Cournia Zoe (Biomedical Research Foundation Academy Of Athens, Greece)
    • 13:00 → 14:00
      Lunch 1h Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
    • 14:00 → 14:30
      Example of successful VI-SEEM application of Molecular Dynamics Simulations: Polyethyleneimine loaded inverse SDS micelle in pentanol/toluene media Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      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 Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
  • Friday, 21 October
    • 09:30 → 11:00
      Hands-on training: Molecular Dynamics Simulations using NAMD: 4. Analyzing MD trajectories Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 11:00 → 12:00
      Introduction to GROMACS Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      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 Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
    • 13:00 → 14:00
      Lunch 1h Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
    • 14:00 → 15:30
      Hands-on training: Computer-Aided Drug Design Room 300

      Room 300

      Belgrade

      Pregrevica 118, 11080 Belgrade, Serbia
      Convener: Zoe Cournia (Biomedical Research Foundation Academy Of Athens, Greece)
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