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The cluster variation method (CVM) is a hierarchy of approximate variational techniques for discrete (Ising–like) models in equilibrium statistical mechanics, improving on the mean–field approximation and the Bethe–Peierls approximation, which can be regarded as the lowest level of the CVM. In recent years it has been applied both in statistical physics and… (More)

- Pierpaolo Bruscolini, Alessandro Pelizzola
- Physical review letters
- 2002

A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Muñoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for a generic protein, for any choice of the energy and entropy parameters, and in principle allows the model to be used… (More)

- Daniele Sciretti, Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Pretti, Alfonso Jaramillo
- Proteins
- 2009

Recent advances in modeling protein structures at the atomic level have made it possible to tackle "de novo" computational protein design. Most procedures are based on combinatorial optimization using a scoring function that estimates the folding free energy of a protein sequence on a given main-chain structure. However, the computation of the… (More)

- Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Zamparo
- The Journal of chemical physics
- 2007

The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein 1BBL, a candidate for downhill folding behavior, and comparing it to the WW domain of protein PIN1, a two-state folder of… (More)

- Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Zamparo
- Physical review letters
- 2007

Previous research has shown a strong correlation of protein folding rates to the native state geometry, yet a complete explanation for this dependence is still lacking. Here we study the rate-geometry relationship with a simple statistical physics model, and focus on two classes of model geometries, representing ideal parallel and antiparallel structures.… (More)

- Mauro Faccin, Pierpaolo Bruscolini, Alessandro Pelizzola
- The Journal of chemical physics
- 2011

We apply the Wako-Saito-Muñoz-Eaton model to the study of myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary variables, provides a finer microscopic detail than the Ising model that has been recently applied to some different… (More)

We consider a variation of the prototype combinatorial-optimisation problem known as graph-colouring. Our optimisation goal is to colour the vertices of a graph with a fixed number of colours, in a way to maximise the number of different colours present in the set of nearest neighbours of each given vertex. This problem, which we pictorially call… (More)

- Marco Zamparo, Alessandro Pelizzola
- Physical review letters
- 2006

We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach, for which we prove that (i) the free energy decreases with time, (ii) the exact equilibrium is recovered in the… (More)

- Richard D Hutton, James Wilkinson, Mauro Faccin, Elin M Sivertsson, Alessandro Pelizzola, Alan R Lowe +2 others
- Journal of the American Chemical Society
- 2015

Protein energy landscapes are highly complex, yet the vast majority of states within them tend to be invisible to experimentalists. Here, using site-directed mutagenesis and exploiting the simplicity of tandem-repeat protein structures, we delineate a network of these states and the routes between them. We show that our target, gankyrin, a 226-residue… (More)

- Marco Zamparo, Alessandro Pelizzola
- The Journal of chemical physics
- 2009

The folding pathways of the B domain of protein A have been the subject of many experimental and computational studies. Based on a statistical mechanical model, it has been suggested that the native state symmetry leads to multiple pathways, highly dependent on temperature and denaturant concentration. Experiments, however, have not confirmed this scenario.… (More)

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