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Atomic-detailed milestones along the folding trajectory of protein G
C. Camilloni, G. Tiana, R. A. Broglia
The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, o…
Exploring the Protein G Helix Free Energy Surface by Solute Tempering Metadynamics
C. Camilloni, D. Provasi, G. Tiana +1
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energ…
Hierarchy of events in protein folding: beyond the Go model
Ludovico Sutto, Guido Tiana, Ricardo A. Broglia
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models i…
What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model
A. Amatori, J. Ferkinghoff-Borg, G. Tiana +1
The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential c…
Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers
R. A. Broglia, G. Tiana, L. Sutto +2
One of the main problems of drug design is that of optimizing the drug--target interaction. In the case in which the target is a viral protein displaying a high mutation rate, a se…
Simple models of protein folding and of non--conventional drug design
R. A. Broglia, G. Tiana
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the thre…