18. VEGA ZZ tutorials
- How to build a small molecule
This tutorial explains how to build a small molecule (e.g. a ligand) using
the 3D molecular editor included in VEGA ZZ and how to perform a systematic
conformational search (grid scan) in order to find the best conformer.
- How to build a small molecule with ISIS/Draw
ISIS/Draw is a great molecular editor but it's able to generate 2D
structure only. In this tutorial, will be explained how to export a molecule
from ISIS/Draw to VEGA ZZ and how to convert it from 2D to 3D.
- Energy minimization of a protein with NAMD
VEGA ZZ allows to prepare the input files for NAMD in easy way without the
use of complex softwares to generate the topology. In this tutorial is explained
step-by-step how to perform a simple conjugate gradients energy minimization
of the crambin crystallographic structure with and without constraints.
- Molecular dynamics of a non-peptic molecule with
NAMD
In this tutorial is explained how to perform the molecular dynamics of the
ibuprofen - water system with NAMD. The ibuprofen is a non-peptidic molecule and
so some potential parameters are missing in the standard CHARMM 22 force field.
The user can learn how to fix the missing force field parameters without the
use of external softwares.
- Molecular docking with VEGA ZZ and Fred
VEGA ZZ, Fred and NAMD are very efficient tools to perform a complete
molecular docking analysis. This tutorial explains in details how was
performed the docking between the farnesyltransferase enzyme (FTase) and a set
of inhibitors as published in the paper: Bolchi C., Pallavicini M., Rusconi
C., Diomede L., Ferri N., Corsini A., Fumagalli L., Pedretti A., Vistoli G.,
Valoti E., "Peptidomimetic inhibitors of farnesyltransferase with high in
vitro activity and significant cellular potency", Bioorg. Med. Chem. Lett.,
17(22), 6192-6 (2007).
- Virtual screening with VEGA ZZ and GriDock
The structure-based virtual screening is a very interesting approach
to find new hit compounds from a database of 3D molecules. In this tutorial,
it's explained how to prepare the input files required by GriDock to find
potential inhibitors of the HIV-1 protease.