By Wilfred F. van Gunsteren, Alexandre M. J. J. Bonvin, Xavier Daura, Lorna J. Smith (auth.), N. Rama Krishna, Lawrence J. Berliner (eds.)
Volume 17 is the second one in a different subject sequence dedicated to sleek strategies in protein NMR, lower than the organic Magnetic Resonance sequence. quantity sixteen, with the subtitle glossy strategies in Protein NMR , is the 1st during this sequence. those volumes current a few of the fresh, major advances within the biomolecular NMR box with emphasis on advancements over the past 5 years. we're commemorated to have introduced jointly in those quantity the various international s premier specialists who've supplied wide management in advancing this box. quantity sixteen includes - vances in huge different types: I. huge Proteins, Complexes, and Membrane Proteins and II. Pulse equipment. quantity 17 includes significant advances in: I. Com- tational equipment and II. constitution and Dynamics. the hole bankruptcy of quantity 17 starts off with a attention of a few vital facets of modeling from spectroscopic and diffraction information by means of Wilfred van Gunsteren and his colleagues. the following chapters take care of mixed automatic assignments and protein constitution choice, a space of severe study in lots of laboratories because the conventional handbook tools are frequently insufficient or exhausting in dealing with huge volumes of NMR information on huge proteins. First, Werner Braun and his affiliates describe their event with the NOAH/DIAMOD protocol built of their laboratory.
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Extra info for Biological Magnetic Resonance: Structure Computation and Dynamics in Protein NMR
This should be remedied by choosing a penalty function which depends on both and : Wilfred F. van Gunsteren et al. , 1995, 1997); see Fig. 5. This is due to the following particular features of NOE distance restraining: 1. Generally, only attractive time-averaged restraints (upper bounds) are used. 2. The van der Waals repulsion between atoms in contact counteracts the attractive restraint. 3. The distance averaging favors short distances, which makes the average follow rapidly the actual value for small r.
1997). Metric tensor effects are negligible (van Gunsteren, 1980) and force-field corrections are not necessary: the dynamics of the molecular system is not affected by the bond-length constraints (van Gunsteren and Karplus, 1982). Use of one of the time-saving methods 1–4 may reduce the computational effort by up to a factor II. Bond-angle bending motion, torsional motion around double bonds, water librational motion In simulations including explicit water molecules, no gain in computational efficiency can be obtained by use of one of the time-saving methods due to the presence of the high-frequency water molecule librations governed by the nonbonded (van der Waals, Coulomb) interactions.
3. Application of multiple-time-step (MTS) algorithms using different time steps or each satisfying condition (22) with respect to the relaxation times and of the different interactions, when integrating the contributions of the different forces. , 1992; Watanabe and Karplus, 1993) and for integrating long-range Coulomb forces separately from the remaining forces in the so-called twin-range method (van Gunsteren and Berendsen, 1990). 4. Softening or smoothing of the high-frequency (most strongly curved) interaction terms in V(r) will also allow the use of longer integration time steps This techique is often used in the earlier stages of structure refinement in order to enlarge the radius of convergence of the restraining minimization and in order to avoid a reduction of when simulating at high temperature in simulated temperature annealing refinement.