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Refining protein models
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Ebook "Principles of protein X-Ray crystallography (Third edition)" provides the theoretical background necessary to understand how the structure of proteins is determined at atomic resolution. It is intended to serve as an introduction for graduate students, postdoctoral researchers, and established scientists who want to use protein crystallography in their own endeavors, or need to understand the subject in order to critically evaluate the literature.
345p
tachieuhoa
28-01-2024
4
2
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GalaxyTBM: Template-based modeling by building a reliable core and refining unreliable local regions
Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate than the single best templates by either combining information from multiple templates or by modeling regions that vary among templates or are not covered by any templates.
8p
viwyoming2711
16-12-2020
10
0
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Recent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. Identifying the correct orientation allows us to study the complex relationship between sequence, structure and the lipid environment, which is otherwise challenging to investigate using experimental techniques due to the difficulty in crystallising membrane proteins embedded within intact membranes.
10p
viwyoming2711
16-12-2020
11
1
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It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models.
8p
vikentucky2711
26-11-2020
11
0
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Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate.
7p
vikentucky2711
24-11-2020
13
1
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Glyoxalase I (gly I) and Glyoxalase II (gly II), zinc-binding enzymes of the glyoxalase pathway, carry out catabolism of methylglyoxal (MG). Gly II gene cloned from Oryza sativa has been widely used in genetic transformation experiments for salinity tolerance. This study could prove useful in further functional characterization of this important protein.
8p
nguathienthan8
20-10-2020
12
2
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Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi -Cαi+1 (θ) and the rotational angle about the Cαi -Cαi+1 bond (τ). Thus, their accurate prediction is useful for structure prediction and model refinement.
8p
viconnecticut2711
28-10-2020
8
0
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As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model refinement, and model assessment.
12p
viconnecticut2711
28-10-2020
25
2
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The X-ray structure of mistletoe lectin I (MLI), a type-II ribosome-inactivatingprotein (RIP), cocrystallized with galactose is described. The model was refined at 3.0 A ˚ resolution to an R-factor of 19.9% using21 899 reflections, with Rfree 24.0%. MLI forms a homodimer (A–B)2in the crystal, as it does in solution at high concentration. The dimer is formed through contacts between the N-terminal domains of two B-chains involvingweak polar and non-polar interactions.
11p
fptmusic
16-04-2013
39
2
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Most agricultural commodities are processed in some way. Some fruits and vegetables are canned, dried or frozen. Meat animals are slaughtered, cut up, and chilled. Wheat is ground, and the flour is baked into bread. Soybeans are crushed, and the oil is made into margarine and shortening; the meal is used for livestock feed or refined for high-protein flour. Cotton is spun into thread and yarn; the yarn goes into cloth, and the cloth into shirts and dresses and sheets. Byproducts of many agricultural products yield glycerin, fatty acids, enzymes, hormones, and many...
23p
nhacchovina
22-03-2013
64
6
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A tri-functional monomeric primase–polymerase domain encoded by the plasmid pIT3 fromSulfolobus solfataricusstrain IT3 was identified using a structural–functional approach. The N-terminal domain of the pIT3 repli-cation protein encompassing residues 31–245 (i.e. Rep245) was modeled onto the crystallographic structure of the bifunctional primase–polymerase domain of the archaeal plasmid pRN1 and refined by molecular dynamics in solution.
14p
galaxyss3
07-03-2013
35
2
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In this study, the crystal structure of a class Cb-lactamase from a psychro-philic organism,Pseudomonas fluorescens, has been refined to 2.2 A ˚ resolu-tion. It is one of the few solved crystal structures of psychrophilic proteins. The structure was compared with those of homologous mesophilic enzymes and of another, modeled, psychrophilic protein.
11p
media19
06-03-2013
31
2
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