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BION web server: predicting non-specifically bound surface ions
2013
Computer applications in the biosciences : CABIOS
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Results: Here, we report a web server, the BION web server, which addresses the demand for tools of predicting surface bound ions, for which specific interactions are not crucial; thus, they are difficult ...
The coordinate file with predicted bound ions is displayed on the output and is available for download. ...
This method is implemented into a web server, the BION web server, which allows predicting non-specific bound ions on the surface of proteins. ...
doi:10.1093/bioinformatics/btt032
pmid:23380591
pmcid:PMC3597141
fatcat:kxjj75pvmjc7rcttmzw2frfeoa
BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics
2020
International Journal of Molecular Sciences
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Here, we report a new release of a computational method, the BION-2 method, that predicts the positions of non-specifically surface-bound ions. ...
Although the role of specifically bound ions ranges from actively providing structural compactness via coordination of charge–charge interactions to numerous enzymatic activities, non-specifically surface-bound ...
In this work, we report a new development of BION [21, 22] , the BION-2, which is a method and a web server to predict non-specifically surface-bound ions. ...
doi:10.3390/ijms22010272
pmid:33383946
pmcid:PMC7794834
fatcat:67rpg4zo7rfklg4k6uglrgp2ta
Ion binding to biological macromolecules
2014
Asian journal of physics : an international quarterly research journal
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It is indicated that specifically bound ions are relatively easier to be revealed while non-specifically associated ions are difficult to predict. ...
In addition, the binding and the residential time of non-specifically bound ions are very much sensitive to the environmental factors in the cells, specifically to the local pH and ion concentration. ...
BION web server-Usually the positions of nonspecific bound ions are on the surface of proteins. ...
pmid:25774076
pmcid:PMC4357017
fatcat:rqutiox4obe67iau2z255hmesa
On the electrostatic properties of homodimeric proteins
2014
Journal of Theoretical and Computational Chemistry
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In addition, the surface points with highest potential are located in the proximity of the interfacial plane of the homodimeric complexes. ...
These findings indicate that frequently homodimerization provides specific electrostatic features needed for the function of proteins. ...
The predictions are based on the magnitude of the electrostatic potential at selected surface-bound grid points and biophysical properties of ions such as radius and charge. ...
doi:10.1142/s0219633614400070
pmid:25419028
pmcid:PMC4238107
fatcat:o3hw34jtxbbiraxlbtwcaw5jy4
Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii CIRM-BIA 129 Mitigate Inflammation by Modulating the NF-κB Pathway
2020
Frontiers in Microbiology
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In silico protein-protein interaction predictions indicated that EV proteins could interact with host proteins, including the immunomodulatory transcription factor NF-κB. ...
Indeed, EVs displayed an anti-inflammatory effect by modulating the NF-κB pathway; this was dependent on their concentration and on the proinflammatory inducer (LPS-specific). ...
For the first method of prediction, EVs and human proteins were submitted to the InterSPPI web server (Lian et al., 2019) , a machine-learning-based predictor. ...
doi:10.3389/fmicb.2020.01544
pmid:32733422
pmcid:PMC7359729
fatcat:lbpmov5oazfmfnvn22p5fgqkui
Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins
[chapter]
2011
Msphere
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PeptideAtlas is a web-accessible database of LC-MS/MS shotgun proteomics results from hundreds of experiments conducted in diverse laboratories. ...
Using the PeptideAtlas web interface, users can browse and search identified peptides and identified proteins, view spectra, and select proteotypic peptides. ...
SpectraST Search: A web server allowing you to perform a spectral library search using the SpectraST software (9) . ...
doi:10.1007/978-1-61779-068-3_23
pmid:21468960
fatcat:hlmawqzo2fevhg7bxid3zn47qm
Abstracts
2019
Journal of Vascular Research
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Angio-HCC score is a novel non-invasive diagnostic tool that could replace AFP in HCC screening and follow up of cirrhotic patients. Abstracts ...
Angio-HCC score produced area under ROC curve of 0.97 for discriminating HCC patients from liver cirrhosis with sensitivity of 89% and specificity of 81% at cutoff 1.5 (i.e., less than 1.5 was considered ...
The experimental data from three protein-peptide dock web servers (CABS-dock, HPEPDOCK and GalaxyWEB) suggest that 10 peptides derived from the N-terminal sequence of mauriporin, have a high affinity towards ...
doi:10.1159/000499516
pmid:34517367
fatcat:umhzslcdnngmldvnguqj2jbn4y
Development of an isobaric-tag based quantitative cross-linking mass spectrometry method
2018
unpublished
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Upon RNA binding, Cas9 undergoes a significant structural rearrangement, where both the free and the RNA bound protein is characterized by x-ray crystallography. ...
Modeling of Cas9 conformations To obtain structural models derived from the identified cross-links, the I-TASSER web server was used. ...
Selected spectra were manually inspected, and almost the complete series of y-and bions could be assigned. ...
doi:10.25365/thesis.51612
fatcat:4qazistnzzbmxfxcoqhkzafsfa
Democracy and Domination in the Law of Workplace Cooperation: From Bureaucratic to Flexible Production
1994
Columbia Law Review
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And they may exercise potent discretion in distributing instrumental rewards or sanctions and psychological affirmation or anxiety in a flexible, non-rule-bound workplace. ...
See Barenberg servers condemned or praised company unionism on just this ground. ...
Individual employers cannot count on capturing the returns to non-firm-specific employee training, including the problemsolving and organizational design skills characteristic of the high-performance workplace ...
doi:10.2307/1123248
fatcat:6i5d2v4dpbgwzotfghvjn6t54e