Computational modeling of biological macromolecules



Computational modeling of biological macromolecules


Rocco Caliandro
Dritan Siliqi
Domenica Di Benedetto* Degree student


Commessa PM.P07.011: Development and application of computational methods for biomolecule structure determination
Modulo I: Development and application of computational methods for structure determination by X-ray diffraction


Molecular dynamics, Molecular modeling, Computational methods

G. Nico, Institute for Calculus Applications, IAC, CNR, Bari, Italy.
A. Cardinali and D. Divenere, Institute of Science of Food Production, ISPA, CNR, Bari, Italy.
P. Carloni, German Research School for Simulation Sciences, Julich, Germany.
X. Cong, G. Rossetti, Statistical and Biological Physics Sector, International School for Advanced Studies, SISSA, Trieste, Italy.
M. Devirgilio, Institute of Vegetal Genetics, IGV, CNR, Bari, Italy.
A. Scilimati, Department Pharmaco-Chemical, University of Bari, Italy
S. Stramaglia, Department of Physics, University of Bari, Italy

The following activities have been recently started:
Comparative modeling to predict the structure of new proteins by using their sequence. The procedure has been applied to a new soluble peroxidase isoenzyme recently extracted and purified from artichoke leaves and to human osteoprotegerin.
Molecular Dynamics simulations to predict the effects of genetic mutations of human prion protein related to neurodegenerative disorders, such as Gerstmann-Sträussler-Scheinker syndrome and familiar Creutzfeldt-Jacob disease.
Computational modeling to predict genetic mutations and selection of sequence fragments to stabilize the folding of recombinant membrane proteins, in order to increase the chances of crystallization.
Development of computational modeling procedures in connection with crystallographic methods directed towards the protein structure determination. The activities include:
ab initio modeling procedures to generate structural models for molecular replacement phasing method;

development of procedures to build structural models from electron density maps;
development of procedures to identify the presence and orientation of α-elices in the Patterson map.

Computational modeling of biological macromolecules  - IMG

Structural predictions by I-TASSER (magenta) and Phyre (cyan) public serves for heme pocket residues of new artichoke leaves peroxidase, superimposed to the crystal structure of the barley grain peroxidase (yellow, PDB code 1BGP)..

Computational modeling of biological macromolecules  - IMG

Structure of human prion protein (PDB code 1HJN).



Rocco Caliandro
Email :
Tel : +39/080/5929150


Last Updated (Thursday, 02 December 2010 16:02)