Tertiary Space
Mostrando 25-36 de 40 artigos, teses e dissertações.
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25. TectoRNA: modular assembly units for the construction of RNA nano-objects
Structural information on complex biological RNA molecules can be exploited to design tectoRNAs or artificial modular RNA units that can self-assemble through tertiary interactions thereby forming nanoscale RNA objects. The selective interactions of hairpin tetraloops with their receptors can be used to mediate tectoRNA assembly. Here we report on the m
Oxford University Press.
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26. Protein folds and families: sequence and structure alignments.
Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a posit
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27. TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints
The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native state. As a step toward addressing both issues, a threading-based method of secondary and tertiary restraint prediction has been developed and applied to ab init
The National Academy of Sciences.
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28. The increased ventilatory response to exercise in chronic heart failure: relation to pulmonary pathology.
OBJECTIVE: To assess the exercise limitation of patients with chronic heart failure (CHF) and its relation to possible pulmonary and ventilatory abnormalities. SETTING: A tertiary referral centre for cardiology. METHODS: The metabolic gas exchange responses to maximum incremental treadmill exercise were assessed in 55 patients with CHF (mean (SD) age 57.9 (1
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29. Three-dimensional structure of fungal proteinase K reveals similarity to bacterial subtilisin.
The three-dimensional structure of the fungal serine protease proteinase K has been determined at 3.3 A resolution by single crystal X-ray diffraction analysis. The enzyme crystallizes in the tetragonal space group P4(3)2(1)2 with cell constants a = b = 68.3 A, c = 108.5 A. The asymmetric unit consists of one monomer of 27 000 daltons mol. wt., approximately
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30. ProteinDBS: a real-time retrieval system for protein structure comparison
We have developed a web server (ProteinDBS) for the life science community to search for similar protein tertiary structures in real time. This system applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. When meanin
Oxford University Press.
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31. Anatomy of protein structures: Visualizing how a one-dimensional protein chain folds into a three-dimensional shape
Here, we depict the anatomy of protein structures in terms of the protein folding process. Via an iterative, top-down dissecting procedure, tertiary structures are spliced down to reveal their anatomy: first, to produce domains (defined by visual three-dimensional inspection criteria); then, hydrophobic folding units (HFU); and, at the end of a multilev
The National Academy of Sciences.
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32. Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution.
The molecular structure of the flavohemoglobin from Alcaligenes eutrophus has been determined to a resolution of 1.75 A and refined to an R-factor of 19.6%. The protein comprises two fused modules: a heme binding module, which belongs to the globin family, and an FAD binding oxidoreductase module, which adopts a fold like ferredoxin reductase. The most strik
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33. Recent improvements in prediction of protein structure by global optimization of a potential energy function
Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimizatio
The National Academy of Sciences.
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34. A genetic algorithm that seeks native states of peptides and proteins.
We describe a computer algorithm to predict native structures of proteins and peptides from their primary sequences, their known native radii of gyration, and their known disulfide bonding patterns, starting from random conformations. Proteins are represented as simplified real-space main chains with single-bead side chains. Nonlocal interactions are taken f
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35. Discriminating compact nonnative structures from the native structure of globular proteins.
Prediction of the native tertiary structure of a globular protein from the primary sequence will require a potential energy model that can discriminate all nonnative structures from the native structure(s). A successful model must distinguish not only alternate structures that are very nonnative but also alternate structures that are compact and near-native.
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36. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
Given the wealth of new RNA structures and the growing list of RNA functions in biology, it is of great interest to understand the repertoire of RNA folding motifs. The ability to identify new and known motifs within novel RNA structures, to compare tertiary structures with one another and to quantify the characteristics of a given RNA motif are major goals
Oxford University Press.