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Rotamer libraries usually contain geometric information to trace an amino acid side chain, atom by atom, onto a protein backbone. These libraries have been widely used in protein design, structure refinement and prediction, homology modeling, an[...]texto impreso
This work investigates the role of N- to C- termini coupling in the folding transition of small, single domain proteins via extensive Monte Carlo simulations of both lattice and off-lattice models. The reported results provide compelling evidenc[...]texto impreso
Improvement of Structure-Based Potentials for Protein Folding by Native and Nonnative Hydrogen Bonds
Pure Go models (where every native interaction equally stabilizes the folded state) have widely proved their convenience in the computational investigation of protein folding. However, a chemistry-based description of the real interactions also [...]texto impreso
The possibility of downhill instead of two-state folding for proteins has been a very controversial topic which arose from recent experimental studies. From the theoretical side, this question has also been accomplished in different ways. Given [...]texto impreso
In recent decades, advances in computational methods and experimental biophysical techniques have improved our understanding of protein folding. Although some of these advances have been remarkable, the structural variability of globular protein[...]texto impreso
Skolnick, Jeffrey ; Kolinski, Andrzej ; Brooks, Charles L. ; Godzik, Adam ; Rey, Antonio | Elsevier | 1993The ability to predict the native conformation of a globular protein from its amino-acid sequence is an important unsolved problem of molecular biology. We have previously reported a method in which reduced representations of proteins are folded[...]texto impreso
One of the major disadvantages of coarse-grained hydrogen bond potentials, for their use in protein folding simulations, is the appearance of abnormal structures when these potentials are used in flexible chain models, and no other geometrical r[...]texto impreso
Flavodoxins are single domain proteins with an alpha/beta structure, whose function and folding have been well studied. Detailed experiments have shown that several members of this protein family present a stable intermediate, which accumulates[...]texto impreso
We describe and test a coarse-grained molecular model for the simulation of the effects of pressure on the folding/unfolding transition of proteins. The model is a structure-based one, which takes into account the desolvation barrier for the for[...]texto impreso
The chaperonin complex GroEL–GroES is able to accelerate the folding process of knotted proteins considerably. However, the folding mechanism inside the chaperonin cage is elusive. Here we use a combination of lattice and off-lattice Monte Carlo[...]texto impreso
We perform extensive lattice Monte Carlo simulations of protein folding to construct and compare the equilibrium and the kinetic transition state ensembles of a model protein that folds to the native state with two-state kinetics. The kinetic de[...]
