Read e-book online Molecular Modeling of Nucleic Acids PDF

By Neocles B. Leontis and John SantaLucia, Jr. (Eds.)

ISBN-10: 0841216460

ISBN-13: 9780841216464

ISBN-10: 0841235414

ISBN-13: 9780841235410

content material: The energetics of nucleotide ionization in water-counterion environments / Harshica Fernando, Nancy S. Kim, George A. Papadantonakis, and Pierre R. LeBreton --
Parameterization and simulation of the actual homes of phosphorothioate nucleic acids / Kenneth E. Lind, Luke D. Sherlin, Venkatraman Mohan, Richard H. Griffey, and David M. Ferguson --
Crystallographic reviews of RNA inner loops / Stephen R. Holbrook --
Hydrogen-bonding styles saw within the base pairs of duplex oligonucleotides / William N. Hunter, Gordon A. Leonard, and Tom Brown --
constitution and balance of DNA containing inverted anomeric facilities and polarity reversals / James M. Aramini, Johan H. van de Sande, and Markus W. Germann --
Conformational research of nucleic acids : difficulties and suggestions / Andrew N. Lane --
NMR constitution selection of a 28-nucleotide sign acceptance particle RNA with entire leisure matrix tools utilizing corrected nuclear Overhauser influence intensities / Peter Lukavsky, Todd M. Billeci, Thomas L. James, and Uli Schmitz --
Molecular modeling of DNA utilizing Raman and NMR information, and the nuclease task of 1,10-phenanthroline-copper ion / W.L. Peticolas, M. Ghomi, A. Spassky, E.M. Evertsz, and T.S. Rush, III --
3-dimensional NOESY-NOESY hybrid-hybrid matrix refinement of a DNA three-way junction / Varatharasa Thiviyanthan, Nishantha Illangasekare, Elliott Gozansky, Frank Zhu, Neocles B. Leontis, Bruce A. Luxon, and David G. Gorenstein --
selection of structural ensembles from NMR info : conformational sampling and likelihood overview / Nikolai B. Ulyanov, Anwer Mujeeb, Alessandro Donati, Patrick Furrer, He Liu, Shauna Farr-Jones, David E. Konerding, Uli Schmitz, and Thomas L. James --
NMR reports of the binding of an SPXX-containing peptide from high-molecular-weight easy nuclear proteins to an A-T wealthy DNA hairpin / Ning Zhou and Hans J. Vogel --
Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays / Jonathan E. Forman, Ian D. Walton, David Stern, Richard P. Rava, and Mark O. Trulson --
RNA folding dynamics : laptop simulations via a genetic set of rules / A.P. Gultyaev, F.H.D. van Batenburg, and C.W.A. Pleij --
An up-to-date recursive set of rules for RNA secondary constitution prediction with more desirable thermodynamic parameters / David H. Mathews, Troy C. Andre, James Kim, Douglas H. Turner, and Michael Zuker --
Modeling of DNA through molecular dynamics simulation : constitution, bending, and conformational t[r]ansitions / D.L. Beveridge, M.A. younger, and D. Sprous --
Molecular dynamics simulations on nucleic acid structures utilizing the Cornell et al. strength box and particle mesh Ewald electrostatics / T.E. Cheatham, III, J.L. Miller, T.I. Spector, P. Cieplak, and P.A. Kollman --
Observations at the A as opposed to B equilibrium in molecular dynamics simulations of duplex DNA and RNA / Alexander D. MacKerell, Jr. --
Modeling duplex DNA oligonucleotides with converted pyrimidine bases / John Miller, Michael Cooney, Karol Miaskiewicz, and Roman Osman --
How the TATA field selects its protein companion / Nina Pastor, Leonardo Pardo, and Harel Weinstein --
RNA tectonics and modular modeling of RNA / Eric Westhof, Benoît Masquida, and Luc Jaeger --
Hairpin ribozyme constitution and dynamics / A.R. Banerjee, A. Berzal-Herranz, J. Bond, S. Butcher, J.A. Esteban, J.E. Heckman, B. Sargueil, N. Walter, and J.M. Burke --
Molecular modeling experiences at the ribosome / Stephen C. Harvey, Margaret S. VanLoock, Thomas R. Rasterwood, and Robert K.-Z. Tan --
Modeling strange nucleic acid buildings / Thomas J. Macke and David A. Case --
computing device RNA third-dimensional modeling from low-resolution facts and multiple-sequence info / François significant, Sébastien Lemieux, and Abdelmjid Ftouhi --
Comparative modeling of the 3-dimensional constitution of sign reputation particle RNA / Christian Zwieb, Krishne Gowda, Niels Larsen, and Florian Müller.

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Strenzke observed that Telmatogeton and allies was a plesiomorphic grouping but, beyond dismembering the Clunioninae, he made no further estimation of its phylogenetic position. 7). The general similarity in habitus of Telmatogeton to Diamesa was noted, but Brundin (1966) confirmed that many characters, including all those of the very generalized larva, the pupal spiraculate thoracic horn, and those of the setose adult (including lack of a postnotal median furrow) were in the plesiomorph state.

The target of complete world inventory is made more elusive by the requirement of users of chironomid taxonomy for descriptions of alllifehistory stages. The responsibility for documentation lies with systematists, who describe, name, classify, identify and elucidate phylogeny and biogeography. Taxonomy, the theory and practice of describing, naming and classifying, is distinguished from systematics, which includes taxonomy but also involves the study of the diversity of and relationships between different organisms.

Species-level information is often lacking. Classifications ought to be predictive, allowing integration and extrapolation of knowledge from well-known species to their lesser-known relatives. However, classifications do not always make sensible predictions: one based upon geographic distribution, pest status or a single life history stage is limited in prediction of other features. Classifications that reflect evolutionary history, or the pattern of nature, have greater predictive value. Several methods are used to deduce pattern and relationships and implement the results into classification.

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Molecular Modeling of Nucleic Acids by Neocles B. Leontis and John SantaLucia, Jr. (Eds.)


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