COVID.si - Skupnostna znanost za boj proti korona virusu

Podlipnik, Črtomir; Jukič, Marko; Nikitina, Natalia; Pleško, Sebastian; Gilardoni, Lorenzo; Tomšič, Gašper; Pevec, Žan; Laba, Boštjan

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Title:	COVID.si - Skupnostna znanost za boj proti korona virusu
Authors:	ID Podlipnik, Črtomir, Univerza v Ljubljani (Author) ID Jukič, Marko (Author) ID Nikitina, Natalia, Institute of Applied Mathematical Research, Karelian Research Center of the Russian Academy of Sciences in Petrozavodsk, Russia (Author) ID Pleško, Sebastian, Univerza v Ljubljani (Author) ID Gilardoni, Lorenzo, University of Milan, Italy (Author) ID Tomšič, Gašper, Univerza v Ljubljani (Author) ID Pevec, Žan (Author) ID Laba, Boštjan (Author)
Files:	https://covid.si/en/ligand-viewer/ Description: Prikazovalnik ligandov - Ligand Viewer https://covid.si/en/stats/ Description: Statistika gruče - Docking statistics https://covid.si/en/quick-start/ Description: Software Download and Quick Start This document has even more files. Complete list of files is available below.
Language:	Slovenian
Work type:	Professional work
Typology:	2.20 - Complete scientific database of research data
Organization:	FKKT - Faculty of Chemistry and Chemical Engineering
Abstract:	Projekt “SKUPNOSTNA ZNANOST IN BOJ PROTI KORONA VIRUSU” je odprt projekt skupnosti dobromislečih raziskovalcev in prostovoljcev, ki želijo s svojim delom, znanjem in izkušnjami, prispevati kamenček v mozaiku poznavanja novega korona virusa in bolezni COVID-19, ki jo ta virus povzroča. Skupino vodita strokovnjaka dr. Črtomir Podlipnik in dr. Marko Jukić, z dolgoletnimi izkušnjami s področja računalniško podprtega načrtovanja molekul, farmacevtske kemije in kemo/bioinformatike. S somišljeniki ter prostovoljci so v zelo kratkem času razvili lastno tehnologijo, ki omogoča porazdeljeno računanje molekulskega sidranja. Tehnologija je osnovana na programčku, ki omogoča povezavo uporabnikovega računalnika s strežnikom, ki porazdeli del knjižnice molekul pripravljenih za molekulsko sidranje (trenutno 10 000 000 spojin). Po končanem sidranju (s programom RxDock), programček pošlje izračunane podatke nazaj na zbirno mesto na strežniku. Po analizi sidranih spojin je končni rezultat seznam molekul s potencialno vezavo na terapevtsko tarčo (v našem primeru so to virusni proteini). Nato lahko preverimo ali so te spojine dobavljive in organiziramo biološko testiranje v sodelovanju z ostalimi raziskovalnimi skupinami. Podatke o nedobavljivih spojinah lahko v nasprotnem primeru posredujemo raziskovalnim skupinam za izvedbo sinteze. V optimalnem scenariju bi lahko identificirali spojine zanimive za farmacevtsko industrijo. Rešitev, ki temelji na porazdeljenem računanju je osnovana na odprtokodnih rešitvah.
Keywords:	COVID-19, virus CoV SARS-2, ligandi, proteini, virusna biokemija, računalniško podprto načrtovanje molekul, molekulsko sidranje, porazdeljeno računanje
Place of publishing:	[S. l.
Publisher:	s. n.
Year of publishing:	2020
PID:	20.500.12556/DKUM-78236
UDC:	578.834
COBISS.SI-ID:	41984771
NUK URN:	URN:SI:UM:DK:4NOTQ8QT
Note:	Sistemske zahteve: pregledovalnik za svetovni splet
Publication date in DKUM:	22.11.2020
Views:	3443
Downloads:	109
Metadata:
Categories:	Misc.
:	PODLIPNIK, Črtomir, JUKIČ, Marko, NIKITINA, Natalia, PLEŠKO, Sebastian, GILARDONI, Lorenzo, TOMŠIČ, Gašper, PEVEC, Žan and LABA, Boštjan, 2020, COVID.si - Skupnostna znanost za boj proti korona virusu [online]. Complete scientific database of research data. 2020. S. l. : s. n. [Accessed 3 April 2025]. Retrieved from: https://covid.si/navodila/ Copy citation

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Licences

License:	CC BY 4.0, Creative Commons Attribution 4.0 International

Link:	http://creativecommons.org/licenses/by/4.0/
Description:	This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:	22.11.2020

Secondary language

Language:	English
Title:	COVID.si - Citizen Science and the fight against the coronavirus
Abstract:	In our project, we are looking for ligands – small molecules that can successfully bind to protein targets and modulate a specific process that is crucial for the virus biochemistry. Together we have developed software that can be easily installed on your computer to help participants help find the cure for today’s invisible enemy. Based on molecular docking, the ideal ligand should be complementary in shape and properties to the binding site of the target biomolecule. Although the complementarity of small molecules is only one prerequisite for the use of a molecule as a drug. The search for the right molecule is best illustrated by finding a small needle in a huge haystack. It is a much more difficult problem because of the number of possible molecular structures. The amount of all possible molecular structures is also called the chemical universe – the size of this abstract space can be estimated to be 10 to the power of 80. There are many galaxies in this chemical universe, and one of the galaxies is a galaxy with potentially pharmacologically active molecules. The method for this purpose is called virtual screening. In principle, the larger the part of the chemical universe that we study, the higher the likelihood of finding a potential cure for the coronavirus.
Keywords:	COVID-19, virus CoV SARS-2, ligands, proteins, virus biochemistry, molecular docking, computer supporting molecular docking, distributed computing