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BION web server: predicting non-specifically bound surface ions

Marharyta Petukh, Taylor Kimmet, Emil Alexov
2013 Computer applications in the biosciences : CABIOS  
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

H. B. Mihiri Shashikala, Arghya Chakravorty, Shailesh Kumar Panday, Emil Alexov
2020 International Journal of Molecular Sciences  
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

Marharyta Petukh, Emil Alexov
2014 Asian journal of physics : an international quarterly research journal  
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

Brandon Campbell, Marharyta Petukh, Emil Alexov, Chuan Li
2014 Journal of Theoretical and Computational Chemistry  
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

Vinícius de Rezende Rodovalho, Brenda Silva Rosa da Luz, Houem Rabah, Fillipe Luiz Rosa do Carmo, Edson Luiz Folador, Aurélie Nicolas, Julien Jardin, Valérie Briard-Bion, Hervé Blottière, Nicolas Lapaque, Gwenaël Jan, Yves Le Loir (+2 others)
2020 Frontiers in Microbiology  
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]

Terry Farrah, Eric W. Deutsch, Ruedi Aebersold
2011 Msphere  
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  
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

Christian Stieger
2018 unpublished
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

Mark Barenberg
1994 Columbia Law Review  
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