Molecular Modeling lab.

Laboratorio di modellistica molecolare, dettaglio

Person in charge: Prof. ssa Laura Bonati

Location: U1, ground floor, room T009 


  • 1 Cluster HP ProLiant (1 dual core Opteron AMD64 storage server; 6 nodes: 4 dual core Opteron AMD64 and 2 quad core Opteron AMD64), operating system: Linux.
  • 5 PC quad core AMD64, operating system: Linux, windows 7.
  • 2 printers


The lab is the venue of Molecular Modeling research group since 2006, the group uses the computational resources here located. The main research activity is the computational approach to study proteins and small molecules at a molecular level.

Programs used:

a) Open source

Modeller: proteins secondary structure prediction by Homology Modelling;
T-Coffee, DALILite, Seaview, and DSSP: for proteins sequence and structure analysis.
Gromacs: Molecular Dynamics simulations.
Pymol and VMD: visualization of molecular structures and dynamics simulations.
R: statistical treatment of data.

b) Licensed

Schrödinger LLC Suite (Maestro, MacroModel, Glide, Prime, etc.), visualization of molecular structures; tools for Molecular Modeling, Molecular Docking, etc.
Amber: Molecular Dynamics simulations on GPU.
Matlab (MathWorks), statistical treatment of data.

Moreover ad hoc tools and scripts are developed to treat data derived from bioinformatics and Molecular Modeling analysis in Python and Bash.

Laboratorio di modellistica molecolare
Molecular Modeling lab.