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

→ Europe/Belgrade
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