By Hin Hark Gan, Tamar Schlick (auth.), Tamar Schlick, Hin Hark Gan (eds.)
REVIEW via ANDRZEJ KLOCZKOWSKI, BAKER middle FOR BIOINFORMATICS AND organic facts, IOWA nation UNIVERSITY
"The authors of the articles within the booklet are the pinnacle experts of their fields and the e-book offers the present state-of-the-art for the extensive spectrum of all at the moment used equipment and methods of macromolecular modeling. The booklet will be very necessary for all readers drawn to the computational modeling of macromolecules. a number of articles within the booklet hide varied features of protein modeling, so i'd hugely suggest this publication to all readers drawn to modeling of proteins."
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Extra resources for Computational Methods for Macromolecules: Challenges and Applications: Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, October 12–14, 2000
J. Med. Chern. 42 ,868-881 (1999) . 100. G . Hummer and A. Szabo, Free energy recons t ruc t ion from non equilibrium single-molecul e pulling expe rime nts . Proc. Natl . A cad. Sci. USA , 98 , 36583661 (2000) . 101. A. R . Leach, Macromolecul ar modelin g: principles and applica ti ons . Addison Wesley Longm an, 1996. 102. H . Hu, R . H. Yun, and J . Hermans, Reversibil ity of free energy simulat ion s: slow gr owt h may have a unique ad vantage . ), Mol. , In Press. 103. B . Isr alewitz , M .
4. The average velocity covariance vector (see text for definition) for each residue of acetylcholinesterase (AChE). The vector lengths are in arbitrary units. The vectors are colored by their length; the longest one being red. The orientation is the same as in Figure 2. ) Mathematics and Molecul ar Neurobiology 37 The vectors reveal how much each residue moves in concert with the gorge. The moiety of AChE that includes the gorge has remarkabl e concerte d motion with the gorg e proper radius. The residues in this moiety gener ally have correlation vectors pointing away from the gorge.
Both t he dielect ric coefficient f and t he screening par am et er K,2 have jump discontinuiti es over surfaces near near t he prot ein-solvent interface. The final discontinuit y is found in t he source t erm f( x ), which mod els the point Mathematics and Molecular Neur obiology 49 charg es at the protein at oms by a sum of delt a fun ctions. While these jump and delt a funct ion discontinuities of coefficient s in the PBE can pose serious numerical difficulties for traditional uniform or nonadaptive mesh par ti al differential equat ion solvers, these features can be efficiently describ ed using adaptive finite element t echniques [34,35,37].