4 papers
The effects of non-native interactions on protein folding rates: Theory and simulation
C. Clementi, S. S. Plotkin
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-nat…
Topological and energetic factors: what determines the structural details of the transition state ensemble and "on-route" intermediates for protein folding? An investigation for small globular proteins
Cecilia Clementi, Hugh Nymeyer, Jose' Nelson Onuchic
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast f…
Folding Lennard-Jones proteins by a contact potential
Cecilia Clementi, Michele Vendruscolo, Amos Maritan +1
We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like h…
Protein Design is a Key Factor for Subunit-subunit Association
Cecilia Clementi, Paolo Carloni, Amos Maritan
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simpl…