Aggrescan3D standalone package for structure-based prediction of protein aggregation properties

2019 ◽  
Vol 35 (19) ◽  
pp. 3834-3835 ◽  
Author(s):  
Aleksander Kuriata ◽  
Valentin Iglesias ◽  
Mateusz Kurcinski ◽  
Salvador Ventura ◽  
Sebastian Kmiecik
Keyword(s):  
Protein Aggregation ◽  
Rational Design ◽  
Protein Solubility ◽  
Automated Analysis ◽  
Computational Framework ◽  
Computational Tools ◽  
Non Profit ◽  
Recent Experimental Study ◽  
The Impact ◽  
Python Package

Abstract Summary Aggrescan3D (A3D) standalone is a multiplatform Python package for structure-based prediction of protein aggregation properties and rational design of protein solubility. A3D allows the re-design of protein solubility by combining structural aggregation propensity and stability predictions, as demonstrated by a recent experimental study. It also enables predicting the impact of protein conformational fluctuations on the aggregation properties. The standalone A3D version is an upgrade of the original web server implementation—it introduces a number of customizable options, automated analysis of multiple mutations and offers a flexible computational framework for merging it with other computational tools. Availability and implementation A3D standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. The A3D standalone source code, wiki with documentation and examples of use, and installation instructions for Linux, macOS and Windows are available in the A3D standalone repository at https://bitbucket.org/lcbio/aggrescan3d.

scholarly journals A3D Database: Structure-based Protein Aggregation Predictions for the Human Proteome

2021 ◽  
Author(s):  
Aleksandra Elzbieta Badaczewska-Dawid ◽  
Javier Garcia-Pardo ◽  
Aleksander Kuriata ◽  
Jordi Pujols ◽  
Salvador Ventura ◽  
...  
Keyword(s):  
Protein Aggregation ◽  
Rational Design ◽  
Structural Information ◽  
Protein Solubility ◽  
Protein Structures ◽  
Human Proteome ◽  
Human Protein ◽  
Database Structure ◽  
Human Disorders ◽  
User Friendly

Motivation: Protein aggregation is associated with highly debilitating human disorders and constitutes a major bottleneck for producing therapeutic proteins. Our knowledge of the human protein structures repertoire has dramatically increased with the recent development of the AlphaFold (AF) deep-learning method. This structural information can be used to understand better protein aggregation properties and the rational design of protein solubility. This article uses the Aggrescan3D (A3D) tool to compute the structure-based aggregation predictions for the human proteome and make the predictions available in a database form. Results: Here, we present the A3D Database, in which we analyze the AF-predicted human protein structures (for over 17 thousand non-membrane proteins) in terms of their aggregation properties using the A3D tool. Each entry of the A3D Database provides a detailed analysis of the structure-based aggregation propensity computed with A3D. The A3D Database implements simple but useful graphical tools for visualizing and interpreting protein structure datasets. We discuss case studies illustrating how the database could be used to analyze physiologically relevant proteins. Furthermore, the database enables testing the influence of user-selected mutations on protein solubility and stability, all integrated into a user-friendly interface. Availability and implementation: A3D Database is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/hproteome

scholarly journals Protocols for rational design of protein solubility and aggregation properties using Aggrescan3D standalone

2020 ◽  
Author(s):  
Aleksander Kuriata ◽  
Aleksandra E. Badaczewska-Dawid ◽  
Jordi Pujols ◽  
Salvador Ventura ◽  
Sebastian Kmiecik
Keyword(s):  
Case Studies ◽  
Rational Design ◽  
Protein Solubility ◽  
Protein Structures ◽  
Three Dimensional ◽  
Computational Tools ◽  
Protein Surfaces ◽  
Amino Acid Mutations ◽  
Protein Variants ◽  
Therapeutics Development

SummaryProtein aggregation is a major hurdle in the development and manufacturing of protein-based therapeutics. Development of aggregation-resistant and stable protein variants can be guided by rational redesign using computational tools. Here, we describe the architecture and functionalities of the Aggrescan3D (A3D) standalone package for the rational design of protein solubility and aggregation properties based on three-dimensional protein structures. We present the case studies of the three therapeutic proteins, including antibodies, exploring the practical use of the A3D standalone tool. The case studies demonstrate that protein solubility can be easily improved by the A3D prediction of non-destabilizing amino acid mutations at the protein surfaces.

МАРКЕТИНГОВІ АСПЕКТИ ФУНКЦІОНУВАННЯ ЛІТЕРАТУРНИХ КОНКУРСІВ ТА ПРЕМІЙ

2020 ◽  
pp. 90
Author(s):  
O. Bondar
Keyword(s):  
Publishing House ◽  
Target Audience ◽  
Point Of View ◽  
Information Support ◽  
Literary Field ◽  
Non Profit ◽  
Functional Aspects ◽  
The Media ◽  
Literary Prizes ◽  
The Impact

<p><em>In this study, I have collected and summarized the functional aspects of a literary prize, contest, and rating, which indicate their affiliation with the marketing complex of the publishing house for the first time. For this purpose, I have analyzed and summarized the common concepts of the functioning of literary prizes and contests as advertising tools for publishing activity. Because the previous studies are only focused on the fact of the impact of the prize on the promotion of editions but do not explain it, these aspects have been considered and introduced by me from the book production’s point of view. I investigated that the prizes and the contests in the literary field are effective marketing tools, which meet many publisher’s needs at the same time and can be considered a non-profit form of capital. I have reviewed the works of other authors, who accept that the economic success of the book is rising if the author is a winner of the literary prize or contest. I have found out that the book prize activates the demand for the book, and the literary contest is a tool to track the reader’s reaction to a future publication. In this way, literary prizes and contests can be considered as a way of conducting a marketing dialogue with the target audience. I have focused on the information support of literary national and international prizes and contests by the media, which attracts attention to the book and forms the reader’s interest. The literary prizes and contests are also considered as a way of exploring trends and their changes, familiarization the popular genres among the target audience and fixation the current choice of modern readers. Literary prizes and contests motivate the authors to improve their literary excellence, are the source of new authors and works, and assist in increasing sales of books. However, further research is recommended.</em></p><strong><em>Key words:</em></strong><em> book prize, book rating, literary contest, literary prize, functions of the literary prizes.</em>

Molecular Design of Peptide-Fc Fusion Drugs

2019 ◽  
Vol 20 (3) ◽  
pp. 203-208 ◽  
Author(s):  
Lin Ning ◽  
Bifang He ◽  
Peng Zhou ◽  
Ratmir Derda ◽  
Jian Huang
Keyword(s):  
Rational Design ◽  
Molecular Design ◽  
Computational Design ◽  
Fusion Technology ◽  
Computational Tools ◽  
Open Questions ◽  
Biological Therapeutics ◽  
Key Steps ◽  
Computational Resources ◽  
Tools And Methods

Background:Peptide-Fc fusion drugs, also known as peptibodies, are a category of biological therapeutics in which the Fc region of an antibody is genetically fused to a peptide of interest. However, to develop such kind of drugs is laborious and expensive. Rational design is urgently needed.Methods:We summarized the key steps in peptide-Fc fusion technology and stressed the main computational resources, tools, and methods that had been used in the rational design of peptide-Fc fusion drugs. We also raised open questions about the computer-aided molecular design of peptide-Fc.Results:The design of peptibody consists of four steps. First, identify peptide leads from native ligands, biopanning, and computational design or prediction. Second, select the proper Fc region from different classes or subclasses of immunoglobulin. Third, fuse the peptide leads and Fc together properly. At last, evaluate the immunogenicity of the constructs. At each step, there are quite a few useful resources and computational tools.Conclusion:Reviewing the molecular design of peptibody will certainly help make the transition from peptide leads to drugs on the market quicker and cheaper.

Here there Be Tygers: Profit, Non-profit, and Loss in the Age of Disintermediation

1997 ◽  
Vol 22 (3) ◽  
Author(s):  
Michael Jensen
Keyword(s):  
Eastern Europe ◽  
Social Institutions ◽  
Scholarly Publishing ◽  
The Political ◽  
Quality Information ◽  
High Quality ◽  
Non Profit ◽  
High Quality Information ◽  
Europe De L’Est ◽  
The Impact

Abstract: Scholarly publishing and access to high-quality information may in fact be threatened, rather than improved, by the revolution in communications, particularly in a fully commercial Internet. The effects of the political revolution in Eastern Europe on scholarship and quality publishing are used as a touchstone of the dangers that occur when naïve revolutionaries make swift changes without fully recognizing the impact upon delicately balanced social institutions such as non-profit organizations. Résumé: La révolution en communications, particulièrement en ce qui regarde un Internet commercialisé, plutôt que d'améliorer l'édition savante et l'accès à de l'information de haute qualité, pourrait en fait poser une menace pour ceux-ci. Cet article examine comment la révolution politique en Europe de l'Est a influé sur la recherche et l'édition de qualité. Il utilise cet exemple pour examiner les dangers que peuvent courir certains révolutionnaires naïfs quand ils instaurent des changements rapides san songer à leur impact sur des institutions sociales à équilibre délicat comme les organisations à but non lucratif.

scholarly journals A cookbook for DNase Hi-C

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Maria Gridina ◽  
Evgeniy Mozheiko ◽  
Emil Valeev ◽  
Ludmila P. Nazarenko ◽  
Maria E. Lopatkina ◽  
...  
Keyword(s):  
Rational Design ◽  
Restriction Enzymes ◽  
Nucleotide Exchange ◽  
Computational Tools ◽  
3 Dimensional ◽  
Cultured Human Cells ◽  
Dna Ends ◽  
By Products ◽  
Robust Protocol

Abstract Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming. Conclusions We propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality.

scholarly journals The Effect of Servant Leadership on Self-Efficacy and Innovative Behaviour: Verification of the Moderated Mediating Effect of Vocational Calling

2021 ◽  
Vol 11 (2) ◽  
pp. 39
Author(s):  
Yunho Ji ◽  
HyunJoong Yoon
Keyword(s):  
Servant Leadership ◽  
Self Efficacy ◽  
Mediating Effect ◽  
Working Environment ◽  
Non Profit ◽  
Vocational Calling ◽  
Conditional Effect ◽  
Innovative Behaviour ◽  
The Impact ◽  
The Relationship

This study aimed to verify the impact of servant leadership on innovative behaviour in non-governmental organisations (NGOs). It particularly investigated the role of a mediator for self-efficacy in the relationship between servant leadership and innovative behaviour. This study defined the organisational psychology-behaviour mechanism in non-profit organisations by verifying the moderated mediating effect of vocational calling in the relationship between servant leadership, self-efficacy, and innovative behaviour. The 174 pilot samples used in this study comprised community service participants in NGOs. The analysis verified the hypothesis set through causal correlations among four variables using regression analysis and the PROCESS macro developed by Hayes. Vocational calling played a moderating role in the relationship between servant leadership and self-efficacy, and vocational calling had a conditional effect on the impact of servant leadership on innovative behaviour through self-efficacy. Meanwhile, self-efficacy fully mediated servant leadership and innovative behaviour. Based on the verification of the mechanism of organisational psychology-action, this study sought ways to develop the organisation of NGOs and improve the working environment.

scholarly journals Effects of the COVID-19 Pandemic on Sports Entrepreneurship

2020 ◽  
Vol 12 (20) ◽  
pp. 8493
Author(s):  
Paloma Escamilla-Fajardo ◽  
Juan M. Núñez-Pomar ◽  
Ferran Calabuig-Moreno ◽  
Ana M. Gómez-Tafalla
Keyword(s):  
Service Quality ◽  
Risk Taking ◽  
Non Profit ◽  
Paired Sample ◽  
Sports Clubs ◽  
Before And After ◽  
The Impact ◽  
The Relationship ◽  
Linear Regressions ◽  
Crisis Situations

Sports entrepreneurship has been considered an important part of sports organisations when overcoming crisis situations. The aim of this study is to determine the impact of the crisis derived from COVID-19 on sports entrepreneurship and whether there are differences in the prediction of entrepreneurship on service quality in non-profit sports clubs. To this end, 145 sports clubs were analysed before and after the outbreak of the virus in society. Paired sample-t tests were carried out to determine the differences in variables studied before (Time I) and after (Time II) the COVID-19 outbreak, and correlations and hierarchical linear regressions were used to analyse the relationship between the variables studied in the two different stages. The results obtained show that risk-taking and innovation are significantly higher after the appearance of COVID-19, while proactivity has not undergone significant changes. Finally, the relationship between sports entrepreneurship and service quality is positive and significant in both stages but stronger before the crisis.

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