scholarly journals The importance of residue‐level filtering, and the Top2018 best‐parts dataset of high‐quality protein residues

2021 ◽  
Author(s):  
Christopher J. Williams ◽  
David C. Richardson ◽  
Jane S. Richardson
Keyword(s):  
Residue Level ◽  
High Quality ◽  
Protein Residues ◽  
High Quality Protein

scholarly journals The importance of residue-level filtering, and the Top2018 best-parts dataset of high-quality protein residues

2021 ◽  
Author(s):  
Christopher J. Williams ◽  
David C. Richardson ◽  
Jane S. Richardson
Keyword(s):  
Protein Design ◽  
Structural Bioinformatics ◽  
Residue Level ◽  
Protein Chain ◽  
High Quality ◽  
3D Protein Structure ◽  
Protein Residues ◽  
Creative Commons ◽  
Reference File ◽  
Acceptable Model

AbstractWe have curated a high-quality, “best parts” reference dataset of about 3 million protein residues in about 15,000 PDB-format coordinate files, each containing only residues with good electron density support for a physically acceptable model conformation. The resulting pre-filtered data typically contains the entire core of each chain, in quite long continuous fragments. Each reference file is a single protein chain, and the total set of files were selected for low redundancy, high resolution, good MolProbity score, and other chain-level criteria. Then each residue was critically tested for adequate local map quality to firmly support its conformation, which must also be free of serious clashes or covalent-geometry outliers. The resulting Top2018 pre-filtered datasets have been released on the Zenodo online web service and is freely available for all uses under a Creative Commons license. Currently, one dataset is residue-filtered on mainchain plus Cβ atoms, and a second dataset is full-residue filtered; each is available at 4 different sequence-identity levels. Here, we illustrate both statistics and examples that show the beneficial consequences of residue-level filtering. That process is necessary because even the best of structures contain a few highly disordered local regions with poor density and low-confidence conformations that should not be included in reference data. Therefore the open distribution of these very large, pre-filtered reference datasets constitutes a notable advance for structural bioinformatics and the fields that depend upon it.The Top2018 dataset provides the first representative sample of 3D protein structure for which excellence of experimental data constrains the detailed local conformation to be correct for essentially all 3 million residues included. Earlier generations of residue-filtered datasets were central in developing MolProbity validation used worldwide, and now Zenodo has enabled anyone to use out latest version as a sound basis for structural bioinformatics, protein design, prediction, improving biomedically important structures, or other applications.

Technology of high quality protein crystals’ obtaining aboard the ISS at execution of joint Japanese–Russian experiments

2020 ◽  
pp. 5-25
Author(s):  
Koji INAKA ◽  
Saori ICHIMIZU ◽  
Izumi YOSHIZAKI ◽  
Kiyohito KIHIRA ◽  
Elena G. LAVRENKO ◽  
...  
Keyword(s):  
Drug Design ◽  
International Space Station ◽  
Space Station ◽  
Protein Crystals ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
High Quality ◽  
International Space ◽  
X Ray ◽  
High Quality Protein

A series of space experiments aboard the International Space Station (ISS) associated with high-quality Protein Crystal Growth (PCG) in microgravity conditions can be considered as a unique and one of the best examples of fruitful collaboration between Japanese and Russian scientists and engineers in space, which includes also other ISS International Partners. X-ray diffraction is still the most powerful tool to determine the protein three dimensional structure necessary for Structure based drug design (SBDD). The major purpose of the experiment is to grow high quality protein crystals in microgravity for X-ray diffraction on Earth. Within one and a half decade, Japan and Russia have established an efficient process over PCG in space to support latest developments over drug design and structural biology. One of the keys for success of the experiment lies in how precisely pre-launch preparations are made. Japanese party provides flight equipment for crystallization and ensures the required environment to support the experiment aboard of the ISS’s Kibo module, and also mainly takes part of the experiment ground support such as protein sample characterization, purification, crystallization screening, and solution optimization for microgravity experiment. Russian party is responsible for integration of the flight items equipped with proteins and precipitants on board Russian transportation space vehicles (Soyuz or Progress), for delivery them at the ISS, transfer to Kibo module, and returning the experiments’ results back on Earth aboard Soyuz manned capsule. Due to close cooperation of the parties and solid organizational structure, samples can be launched at the ISS every half a year if the ground preparation goes smoothly. The samples are crystallized using counter diffusion method at 20 degree C for 1–2.5 months. After samples return, the crystals are carefully taken out from the capillary, and frozen for X-ray diffraction at SPring8 facility in Japan. Extensive support of researchers from both countries is also a part of this process. The paper analyses details of the PCG experiment scheme, unique and reliable technology of its execution, and contains examples of the application. Key words: International Space Station, Protein crystals, Microgravity, International collaboration.

scholarly journals Heterosis in crosses among white grain maize populations with high quality protein

2006 ◽  
Vol 41 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Márcio Costa Rodrigues ◽  
Lázaro José Chaves ◽  
Cleso Antônio Patto Pacheco
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Least Square ◽  
Superior Performance ◽  
Normal Equation ◽  
High Quality ◽  
Maize Populations ◽  
High Quality Protein ◽  
Female Flowering ◽  
White Grain

The objective of this work was to investigate heterosis and its components in 16 white grain maize populations presenting high quality protein. These populations were divided according to grain type in order to establish different heterosis groups. The crosses were carried out according to a partial diallel cross design among flint and dent populations. Seven agronomic traits were evaluated in three environments while four leaf diseases and incidence of corn stunt were evaluated in one. Least square procedure was applied to the normal equation X'Xbeta = X'Y, to estimate the model effects and their respective sum of squares. Among the heterosis components, in diallel analysis, significance for average heterosis in grain yield, number of days to female flowering and to all evaluated diseases was detected. Specific heterosis was significant for days to female flowering and resistance to Puccinia polysora. Results concerned to grain yield trait indicate that populations with superior performance in dent group, no matter what flint population group is used in crosses, tend to generate superior intervarietal hybrids. In decreasing order of preference, the dent type populations CMS 476, ZQP/B 103 and ZQP/B 101 and the flint type CMS 461, CMS 460, ZQP/B 104 and ZQP/B 102 are recommended to form composites.

scholarly journals High quality protein crystal growth under microgravity in JAXA PCG project

2011 ◽  
Vol 67 (a1) ◽  
pp. C460-C460
Author(s):  
M. Sato ◽  
H. Tanaka ◽  
K. Inaka ◽  
S. Sano ◽  
M. Masaki ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Protein Crystal ◽  
High Quality ◽  
High Quality Protein ◽  
Protein Crystal Growth

scholarly journals FALCON2: a web server for high-quality prediction of protein tertiary structures

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lupeng Kong ◽  
Fusong Ju ◽  
Haicang Zhang ◽  
Shiwei Sun ◽  
Dongbo Bu
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Web Server ◽  
High Quality ◽  
Tertiary Structures ◽  
Target Proteins ◽  
High Quality Protein ◽  
Protein Functions

Abstract Background Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions. We have designed two approaches to protein structure prediction, including a template-based modeling approach (called ProALIGN) and an ab initio prediction approach (called ProFOLD). Briefly speaking, ProALIGN aligns a target protein with templates through exploiting the patterns of context-specific alignment motifs and then builds the final structure with reference to the homologous templates. In contrast, ProFOLD uses an end-to-end neural network to estimate inter-residue distances of target proteins and builds structures that satisfy these distance constraints. These two approaches emphasize different characteristics of target proteins: ProALIGN exploits structure information of homologous templates of target proteins while ProFOLD exploits the co-evolutionary information carried by homologous protein sequences. Recent progress has shown that the combination of template-based modeling and ab initio approaches is promising. Results In the study, we present FALCON2, a web server that integrates ProALIGN and ProFOLD to provide high-quality protein structure prediction service. For a target protein, FALCON2 executes ProALIGN and ProFOLD simultaneously to predict possible structures and selects the most likely one as the final prediction result. We evaluated FALCON2 on widely-used benchmarks, including 104 CASP13 (the 13th Critical Assessment of protein Structure Prediction) targets and 91 CASP14 targets. In-depth examination suggests that when high-quality templates are available, ProALIGN is superior to ProFOLD and in other cases, ProFOLD shows better performance. By integrating these two approaches with different emphasis, FALCON2 server outperforms the two individual approaches and also achieves state-of-the-art performance compared with existing approaches. Conclusions By integrating template-based modeling and ab initio approaches, FALCON2 provides an easy-to-use and high-quality protein structure prediction service for the community and we expect it to enable insights into a deep understanding of protein functions.

scholarly journals Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals

2018 ◽  
Vol 115 (14) ◽  
pp. 3634-3639 ◽  
Author(s):  
Ryo Suzuki ◽  
Haruhiko Koizumi ◽  
Keiichi Hirano ◽  
Takashi Kumasaka ◽  
Kenichi Kojima ◽  
...  
Keyword(s):  
Glucose Isomerase ◽  
Dynamical Theory ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
High Quality ◽  
Rocking Curve ◽  
Dynamical Diffraction ◽  
High Quality Protein ◽  
Good Agreement

High-quality protein crystals meant for structural analysis by X-ray diffraction have been grown by various methods. The observation of dynamical diffraction in protein crystals is an interesting topic because dynamical diffraction generally occurs in perfect crystals such as Si crystals. However, to our knowledge, there is no report yet on protein crystals showing clear dynamical diffraction. We wonder whether the perfection of protein crystals might still be low compared with that of high-quality Si crystals. Here, we present observations of the oscillatory profile of rocking curves for protein crystals such as glucose isomerase crystals. The oscillatory profiles are in good agreement with those predicted by the dynamical theory of diffraction. We demonstrate that dynamical diffraction occurs even in protein crystals. This suggests the possibility of the use of dynamical diffraction for the determination of the structure and charge density of proteins.

Effects of dairy and plant protein on growth and growth biomarkers in a piglet model

2021 ◽  
Author(s):  
Anne Krogh Ingerslev ◽  
Laura Rasmussen ◽  
Pan Zhou ◽  
Jan Værum Nørgaard ◽  
Peter Kappel Theil ◽  
...  
Keyword(s):  
Living Conditions ◽  
Human Nutrition ◽  
Plant Protein ◽  
World Population ◽  
Food Protein ◽  
High Quality ◽  
Protein Sources ◽  
High Quality Protein

The increasing world population with improved living conditions has increased the demand for food protein. This has intensified the search for sustainable alternative plant-derived high-quality protein sources for human nutrition....

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