Daniel R. Ripoll

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An efficient method has been developed for packing alpha-helices in proteins. It treats alpha-helices as rigid bodies and uses a simplified Lennard-Jones potential with Miyazawa-Jernigan contact-energy parameters to describe the interactions between the alpha-helical elements in this coarse-grained system. Global conformational searches to generate packing(More)
Polysialic acid (PSA) is a major regulator of cell-cell interactions in the developing nervous system and in neural plasticity in the adult. As a polyanionic molecule with high water-binding capacity, PSA increases the intercellular space generating permissive conditions for cell motility. PSA enhances stem cell migration and axon path finding and promotes(More)
Global optimization is playing an increasing role in physics, chemistry, and biophysical chemistry. One of the most important applications of global optimization is to find the global minima of the potential energy of molecules or molecular assemblies, such as crystals. The solution of this problem typically requires huge computational effort. Even the(More)
Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five beta-strands flanked by two alpha-helices is common(More)
A hierarchical approach based exclusively on finding the global minimum of an appropriate potential energy function, without the aid of secondary structure prediction, multiple-sequence alignment, or threading, is proposed. The procedure starts from an extensive search of the conformational space of a protein, using our recently developed united-residue(More)
A general protocol for refining the parameters of macromolecular potential energy functions by optimizing criteria that compare nativelike and nonnative conformations of one or more benchmark protein(s) is described. The protocol exploits the high efficiency of conformational space annealing (CSA) in finding the lowest-energy conformation of an isolated(More)
Protein folding is a very difficult global optimization problem. Furthermore it is coupled with the difficult task of designing a reliable force field with which one has to search for the global minimum. A summary of a series of optimization methods developed and applied to various problems involving polypeptide chains is described in this paper. With(More)
In recent years several approaches have been proposed to overcome the multiple minima problem associated with non-linear optimization techniques used in the analysis of molecular conformations. One such technique based on a parallel Monte Carlo search algorithm is analysed. Experiments on the Intel iPSC/2 confirm that the attainable parallelism is limited(More)
The development of three physics-based energy functions (force fields), designed to simulate the restricted free energy of proteins of the R, , and R/ structural classes, is described. Each force field corresponds to a particular weighting of the united-residue (UNRES) interactions defined in earlier work. 1-6 To find the optimal weights for the R, , and R/(More)
For enveloped viruses, fusion of the viral envelope with a cellular membrane is critical for a productive infection to occur. This fusion process is mediated by at least three classes of fusion proteins (Class I, II, and III) based on the protein sequence and structure. For Rift Valley fever virus (RVFV), the glycoprotein Gc (Class II fusion protein)(More)