Folding Lennard-Jones proteins by a contact potential

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dc.creatorClementi, Cecilia
dc.creatorVendruscolo, Michele
dc.creatorMaritan, Amos
dc.creatorDomany, Eytan
dc.date1999-02-16
dc.date.accessioned2026-07-07T03:12:49Z
dc.date.available2026-07-07T03:12:49Z
dc.descriptionWe 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 heteropolymer sequences, whose lowest energy (native) conformations were then identified by Molecular Dynamics. Then we turned to investigate whether one can find a pairwise contact potential, whose ground states are the contact maps associated with these native conformations. We show that such a requirement cannot be satisfied exactly - i.e. no such contact parameters exist. Nevertheless, we found that one can find contact energy parameters for which an energy minimization procedure, acting in the space of contact maps, yields maps whose corresponding structures are close to the native ones. Finally we show that when these structures are used as the initial point of a Molecular Dynamics energy minimization process, the correct native folds are recovered with high probability.
dc.descriptionsubmitted to "Proteins: Structure, Function, and Genetics"
dc.identifierhttps://arxiv.org/abs/cond-mat/9902228
dc.identifierhttp://arxiv.org/abs/cond-mat/9902228
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/29062
dc.subjectStatistical Mechanics
dc.subjectQuantitative Biology
dc.titleFolding Lennard-Jones proteins by a contact potential
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