Download Advances in Chemical Physics, Computational Methods for by Richard A. Friesner, Ilya Prigogine, Stuart A. Rice PDF

By Richard A. Friesner, Ilya Prigogine, Stuart A. Rice

Because the first makes an attempt to version proteins on a working laptop or computer begun nearly thirty years in the past, our realizing of protein constitution and dynamics has dramatically elevated. Spectroscopic dimension thoughts proceed to enhance in answer and sensitivity, permitting a wealth of data to be got with reference to the kinetics of protein folding and unfolding, and complementing the distinct structural photo of the folded nation. at the same time, algorithms, software program, and computational have advanced to the purpose the place either structural and kinetic difficulties should be studied with a good measure of realism. regardless of those advances, many significant demanding situations stay in realizing protein folding at either the conceptual and sensible degrees. Computational tools for Protein Folding seeks to light up contemporary advances in computational modeling of protein folding in a fashion that may be valuable to physicists, chemists, and chemical physicists. overlaying a large spectrum of computational equipment and practices culled from numerous examine fields, the editors current an entire variety of versions that, jointly, offer a radical and present description of all points of protein folding. A priceless source for either scholars and execs within the box, the e-book might be of worth either as a state of the art evaluate of latest info and as a catalyst for uplifting new experiences. Computational equipment for Protein Folding is the one hundred and twentieth quantity within the acclaimed sequence Advances in Chemical Physics, a compilation of scholarly works devoted to the dissemination of up to date advances in chemical physics, edited by way of Nobel Prize-winner Ilya Prigogine.

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Extra resources for Advances in Chemical Physics, Computational Methods for Protein Folding (Volume 120)

Example text

Although rcv values for the various descriptors obtained from the secondary structure prediction program (indices 16 to 21 in Table I) are lower than those for measures of the known native structure (indices 6 to 15), the former correlations may be sufficiently high that the calculated descriptors could be used to identify particularly fast or slow proteins without the need for highresolution structures. The stability, which has been suggested to be of importance based on model studies, exhibits no clear relation to the folding rate.

Although doing so requires investigation of the kinetics of particular proteins at the level of individual residues, for which protein engineering [4] and nuclear magnetic resonance (NMR) [5] experiments are very useful, complementary information about the roles played by the sequence and the structure can also be obtained by a statistical analysis of the folding rates of a series of proteins. Statistical methods have been applied for many years in attempts to predict the structures of proteins (for a review of progress in this area, see the chapter by Meller and Elber, this volume), but their use in the analysis of folding kinetics is relatively recent.

An alternative phenomenological model was developed by Debe and Goddard [47]. In essence, they assumed a sequence of events which is, in a certain sense, the reverse of the diffusion–collision model [48,49]: the correct overall (tertiary) structure is formed at low-resolution first by a random search and then local (secondary) refinement takes place within the manifold of states in that fold. Thus, the factor that determines the relative rate of folding for a series of proteins is the probability of randomly sampling a structure with the known native contacts (estimated by a Monte Carlo procedure); the distance at which a contact was counted was adjusted to optimize the fit.

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