More info about the science of the project

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manalog

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Message 228 - Posted: 7 Dec 2020, 9:15:43 UTC

Hello,
it's always a great news when a new Boinc project starts, and even more it is a great news that this new project is going to fight Coronavirus. Nonetheless I have some questions before being sure that it is worthy to dedicate some of my (small) hardware resources to this project:

1) It's very nice to see the face of the people working on this project on https://covid.si/en/team/. But, I wonder, is this an "independent" project managed by these people or is it affiliated to one or more academic institutes?
2) There is a very similar project on Worldcommunitygrid, Open Pandemics. They are testing ZINC database against several targets of the virus and their computing power is much higher than here. Of course redundancy in science is a good thing, but is this project different in some way or is it testing the same molecules and targets of OpenPandemics? And perhaps the same of Ibercivis too?
3) What is RXDock? (And CurieMariedock too?) Is it opensource? In which way is it different/better/worse than the well known Autodock?
4) What are the aims of this project? Of course the first is to find a molecule capable to inhibit the replication of the virus, but then are there some "collateral" things that could help science in other ways too and even if this project won't be "the" project that will defeat coronavirus? I think for example: developing of new software, advances in basic fields of bioinformatics, consolidation of a new researchers group in Europe/Eastern Europe/Russia and so on.
5) What do you expect from this project? That is, what do you think will it happen in 6 months - 1 year? Are you working on some publication?
6) Will the results be released as open science?

Than you and sorry for my English.
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Message 232 - Posted: 8 Dec 2020, 11:26:18 UTC - in response to Message 228.  

Dear manalog,

We will try to answer your questions below:

1) "Hello,

it's always a great news when a new Boinc project starts, and even more it is a great news that this new project is going to fight Coronavirus. Nonetheless I have some questions before being sure that it is worthy to dedicate some of my (small) hardware resources to this project:"

We are indeed grateful for You all helping us all out. Every individual is key to the success of the complete project and we think shared science and/or community-science is the key to the future. Successful communication between science and the community is also the way good information can be accessed and disseminated to the community.

2) "It's very nice to see the face of the people working on this project on https://covid.si/en/team/. But, I wonder, is this an "independent" project managed by these people or is it affiliated to one or more academic institutes? "

Well, this was a small organic project that started over beer between colleagues in the field of drug design and medicinal chemistry here in Slovenija. We were discussing how to help and humbly started on a small project. In time this was born. The project slowly grew and as we are all in academic institutions, we also got support from them. So Yes, the affiliations are University of Maribor, University of Ljubljana, CTK Ljubljana, Karelian Research Center of the Russian Academy of Sciences,.. namely our primary institutions. But as we work in the field, we have a broad international affiliations that we work with, and we have support from other research groups and laboratories across the world. Namely, now we work on getting support from synthesis and biology groups to get testing capabilities on isolated proteins as well as on cell lines. In the future we aim to produce compounds that have activity on physical systems to serve as probes for viral research or leads for possible drug design.

3) "There is a very similar project on Worldcommunitygrid, Open Pandemics. They are testing ZINC database against several targets of the virus and their computing power is much higher than here. Of course redundancy in science is a good thing, but is this project different in some way or is it testing the same molecules and targets of OpenPandemics? And perhaps the same of Ibercivis too?"

Yes in science many topics are studied in parallel and our project is only one of the many options proposed by the community, e.g. JEDI Grand Challenge and so on. We are not completely familiar with OpenPandemics and Ibercivis CORONA projects but I guess we are similar. We see that OpenPandemics is doing many much needed approaches and Ibercivis CORONA project is starting out also on good basis. What We can tell You for sure is this: We are a focused group of drug design scientists that aim to perform a focused set of scientific projects on focused targets (now it is only 3CLpro, next target is carefully studied). We aim to construct ever increasing libraries of compounds to cover novel chemical space. We aim to place the compounds for biological evaluation. Last but not least, we aim to be transparent and work with the community.

4) "What is RXDock? (And CurieMariedock too?) Is it opensource? In which way is it different/better/worse than the well known Autodock?"

Molecular Docking is a complex and multifaceted problem and there are many computational tools for the job. Autodock, Autodock VINA, Glide, Fred, DOCK, Gold are only a few examples. It is hard to directly compare different solutions as the tool is only as good as the system you are studying. The tools are often complementary and You have to test the tools on the studied system. Regarding RXDock or RDock the story is:
The RiboDock program was developed from 1998 to 2006 by the software team at RiboTargets (subsequently Vernalis (R&D) Ltd). In 2006, the software was licensed to the University of York for maintenance and distribution under the name rDock.
In 2012, Vernalis and the University of York agreed to release the program as open-source software. This version is developed with support from the University of Barcelona -- sourceforge.net/projects/rdock. The development of rDock stalled in 2014. Since 2019, RxTx is developing a fork of rDock under the name RxDock (open source). In order to implement new features, optimise and utilise modern hardware, from 2020, a fork of RxDock is developed under the name CmDock or CurieMarie Dock and it is indeed opensource.

We studied Rdock or RxDock (code update and rewrite and is able to be nicely compiled on modern OS-es) on our research systems and we got good results and decided to apply this solution. For the reference RDock was also successfully applied in early corona research in an excellent Galaxy project. Furthermore, as we are software developers also, we identified further possible software optimizations and in order to implement new features and QOL improvements (GPU support), we decided to fork the project and create a novel CmDock platform to bring the software up to speed (no pun intended :)).

5) "What are the aims of this project? Of course the first is to find a molecule capable to inhibit the replication of the virus, but then are there some "collateral" things that could help science in other ways too and even if this project won't be "the" project that will defeat coronavirus? I think for example: developing of new software, advances in basic fields of bioinformatics, consolidation of a new researchers group in Europe/Eastern Europe/Russia and so on."

As You eloquently put it already. Yes we aim for many more collateral results. Firstly, main scientific contributions, secondly the development and optimization of the software, thirdly the establishment and consolidation of a drug design community and research group in order to tackle also future or other health problems. We would be most happy if We could bring results about SARS-CoV-2 but also tackle other medicinal chemistry problems together in the future.

Lastly, -indeed, to bring some advances to the field of bioinformatics, but this is a hard question and a problem. Yes some of us are working a lot on bioinformatics methodology also; Mainly how to bring additional quality data into HTVS such as water data and additional exp. data,.... So to join this to this project this would be the ultimate reward to us and to the community: to bring some new insight to basic bioinformatics science.

6) "What do you expect from this project? That is, what do you think will it happen in 6 months - 1 year? Are you working on some publication? "

Yes, we are working on publications already in our basic institutions and of course on the joint COVID.SI/SIDOCK project where we expect the first in silico publications to be available in early 21. In a Year we hope for experimental hit compounds, biology collaboration and an established community where we together tackle the drug design problems and communicate with each other.

7) "Will the results be released as open science?"

Indeed we hope to also contribute to OpenScience.

8) "Thank you and sorry for my English."

We hope we answered your questions and thanks to You and to all of the participants for support. We hope we work more in the future.

Marko Jukic
Natalia Nikitina
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Message 234 - Posted: 8 Dec 2020, 16:30:20 UTC - in response to Message 232.  

This is one of the best explanation of a Boinc project to the community I have ever seen, thank you so much, it is evident that you take care of your community and I hope we will be able to provide you a good amount of computational power.
It's very cool you are working on a GPU client too.
I will try to spread the voice as much as possible.
Matteo
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Message 235 - Posted: 8 Dec 2020, 16:36:59 UTC - in response to Message 234.  

Dear Mateo,

I agree with you Marko and Natalia did really nice recap of our project.

I have idea to publish this answer as interview in our site https://covid.si maybe we will also translate interview to Slovenian language.

What do you think?

Crtomir
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Message 236 - Posted: 8 Dec 2020, 16:50:44 UTC - in response to Message 235.  

Absolutely no problem. If you like I can make a translation in Italian too
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Message 237 - Posted: 8 Dec 2020, 17:14:25 UTC - in response to Message 236.  

Excellent
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Message 238 - Posted: 8 Dec 2020, 19:06:10 UTC - in response to Message 236.  

Published in COVID.SI:

https://covid.si/interview-of-boinc-user/
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Message 239 - Posted: 8 Dec 2020, 19:50:58 UTC - in response to Message 236.  

Absolutely no problem. If you like I can make a translation in Italian too


It's a great idea! Then we will put it into Italian language's section of the site.

We even have here a Russian enthusiast who can make translations to Italian and will love to, and you could be our expert and check :)
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Message 240 - Posted: 8 Dec 2020, 20:54:58 UTC - in response to Message 238.  

Published in COVID.SI:

https://covid.si/interview-of-boinc-user/

Wow, great!
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Message 250 - Posted: 11 Dec 2020, 23:11:56 UTC - in response to Message 240.  

Here is it :) :)
It's a honor to do this job for such a noble cause:

Intervista riguardo il progetto Boinc SiDock@Home

Matteo: La nascita di un nuovo progetto Boinc è sempre un’ottima notizia, e lo è ancora di più se il progetto ha come scopo la lotta contro il coronavirus. Nonostante ciò, vorrei porre qualche domanda prima di poter essere certo che valga la pena dedicare un po’ delle mie, seppur limitate, risorse hardware al progetto.

Marko & Natalia: Siamo particolarmente grati che voi tutti ci stiate aiutando. Ciascun individuo è la chiave per il successo dell’intero progetto e crediamo che la scienza condivisa e/o la scienza comunitaria sia la chiave per il futuro. Una comunicazione di successo tra comunità scientifica e volontari è anche un esempio di come informazioni utili possano essere rese disponibili e diffuse a tutta la comunità.

Matteo: È davvero bello che sia possibile vedere i volti delle persone che lavorano a questo progetto alla pagina https://covid.si/en/team/. Tuttavia, mi chiedo se questo sia un progetto “indipendente” (gestito da queste persone) oppure se sia affiliato con una o più istituzioni accademiche.

Marko & Natalia: Il progetto è iniziato con un piccolo organico, cominciando durante una birra tra colleghi nel campo dello sviluppo di farmaci e di chimica medica qui in Slovenia: stavamo discutendo su come potessimo aiutare in questa situazione e, con modestia, abbiamo avviato un piccolo progetto che con il tempo è nato e cresciuto. Dal momento che siamo tutti in istituzioni accademiche, abbiamo anche ricevuto supporto da queste; quindi, per rispondere alla domanda, si: i nostri principali riferimenti sono Università di Maribor, Università di Ljubljana, CTK Ljubljana e il Karelian Research Center della Russian Academy of Sciences. Tuttavia, mentre procediamo con il lavoro, abbiamo una rete internazionale con cui cooperiamo e siamo supportati da altri gruppi di ricerca e laboratori sparsi in tutto il mondo. In particolare, ora stiamo lavorando per ottenere supporto dai gruppi di sintesi e di biologia per ottenere strutture di test su proteine isolate e su linee cellulari. Nel futuro, vogliamo progettare e produrre composti che abbiano attività sui sistemi fisici e possano funzionare da sonde per la ricerca di virus o come strutture guida per lo sviluppo di farmaci.

Matteo: Esiste un progetto molto simile sulla piattaforma World Community Grid: Open Pandemics – COVID 19( https://www.worldcommunitygrid.org/research/opn1/overview.do ) che sta testando il database ZINC (https://zinc15.docking.org/) contro diversi obiettivi strategici del virus, e la loro potenza di calcolo è decisamente superiore rispetto a quella all’opera in questo progetto. Nonostante la ridondanza nelle ricerche scientifiche sia un’ottima cosa, mi chiedo: questo progetto è in qualche modo diverso da OpenPandemics o sta testando le stesse molecole contro gli stessi target? E magari sono anche gli stessi di Ibercivis?

Marko & Natalia: Si, in effetti nella ricerca scientifica molte questioni vengono studiate in parallelo e il nostro progetto è una delle tante opzioni proposte dalla comunità scientifica, come lo JEDI Grand Challenge (https://www.covid19.jedi.group/ ). Non siamo del tutto familiari con i progetti OpenPandemics e Ibercivis CORONA, ma penso che siamo simili. Osserviamo che OpenPandemics ha molti approcci decisamente necessari per questa ricerca e anche il progetto Ibercivis CORONA sta partendo su ottime basi. Ciò che possiamo dirti con certezza è questo: siamo un gruppo di scienziati del campo dello sviluppo farmaci, focalizzati nel condurre una serie di progetti scientifici su particolari target del virus (al momento il 3Clpro, stiamo accuratamente studiando il prossimo target). I nostri obiettivi sono quelli di compilare una libreria di composti sempre più estesa, che possa coprire i nuovi spazi chimici, e anche quello di testare i composti per una sperimentazione e valutazione biologica. Infine, vogliamo essere trasparenti e collaborare con la comunità.

Matteo: Cos’è RXDock? E CurieMariedock? È software libero? In che modo sono diversi/migliori/peggiori rispetto al noto Autodock?

Marko & Natalia: Il docking molecolare è un problema complesso e sfaccettato ed esistono molti strumenti di calcolo per questo tipo di compito: Autodock, Autodock VINA, Glide, Fred, DOCK, Gold sono alcuni esempi. Non è facile comparare direttamente le diverse soluzioni tra di loro nella misura in cui ciascuno strumento è tanto utile quanto utile è il sistema che si sta studiando. Questi applicativi sono spesso complementari e occorre testarli sui sistemi che si stanno studiando. Questa è la storia di rxDock o rDock:
L’applicativo RiboDock è stato sviluppato dal 1998 al 2006 dal software team RiboTargets (dopo Vernalis(R&D) Ltd.). Nel 2006 il software è stato concesso sotto licenza all’Università di York per mantenerlo e distribuirlo sotto il nome rDock.
Nel 2012 Vernalis e l’Università di York si sono accordate per rilasciare il programma sotto una licenza libera. Questa versione open source è sviluppata con il supporto dell’Università di Barcellona sourceforge.net/projects/rdock. Lo sviluppo di rDock è cessato nel 2014 e dal 2019 RxTx sta sviluppando una derivazione di rDock dal nome rxDock, sempre open source. Una ulteriore derivazione, sempre libera, di RxDock, dal nome CmDock o CurieMarie Dock viene sviluppata a partire dal 2020, con l’obiettivo di implementare nuove caratteristiche e ottimizzare l’utilizzo di hardware più recente.
Abbiamo studiato Rdock/RxDock (il codice aggiornato e riscritto può essere perfettamente compilato su un sistema operativo moderno) sui nostri elaboratori e, avendo ottenuto buoni risultati, abbiamo deciso di usare questa soluzione. Come riferimento, rDock è stato anche utilizzato con successo durante le ricerche iniziali sul coronavirus dall’eccellente progetto Galaxy Project. Dal momento che siamo anche sviluppatori software, abbiamo identificato ulteriori possibili ottimizzazioni e, allo scopo di aggiungere nuove funzioni e miglioramenti della qualità (come il supporto alle GPU – Processori grafici accelerati), abbiamo deciso di sviluppare una derivazione del progetto e creare una nuova piattaforma, CmDock, per mantenere il software aggiornato (nessun gioco di parole :))

Matteo: Quali considerate che siano gli obiettivi del progetto? Ovviamente il primo obiettivo sarebbe quello di trovare una molecola capace di inibire la replicazione del virus, mi chiedo però se ci sia un “qualcosa in più” che possa aiutare gli scienziati in altre maniere, anche nel caso questo progetto non sia quello capace di sconfiggere il coronavirus. Penso ad esempio allo sviluppo di nuovo software, progressi in aree fondamentali della bioinformatica, oppure il consolidamento di un nuovo gruppo di ricercatori in Europa / Europa dell’Est / Russia e così via…

Marko & Natalia: Si, in effetti stiamo puntando a tantissimi ulteriori risultati collaterali. Per prima cosa, il principale contributo scientifico; in secondo luogo, lo sviluppo e l’ottimizzazione del software; inoltre, lo sviluppo e il consolidamento di una comunità di sviluppatori di farmaci e un gruppo di ricerca capace di affrontare futuri o ulteriori problemi sanitari. Saremmo molto lieti di esaminare congiuntamente i risultati sulla SARS-CoV-2, ma anche altri problemi medico-chimici in futuro.
Infine, abbiamo intenzione di apportare possibilmente qualche progresso nei campi dell’informatica chimica e della bioinformatica e trasmettere le nostre conoscenze ai ricercatori più giovani. Si, qualcuno di noi sta anche lavorando parecchio sui metodi bioinformatici, [in particolare come integrare quality data aggiuntivi nell’HTVS, come dati sull’acqua e additional exp ( NDT this part is a bit technical, should be rechecked by someone else).]

Matteo: Cosa vi aspettate da questo progetto? Nel senso, cosa pensate che possa succedere nell’arco di sei mesi, un anno? State lavorando su qualche articolo?

Marko & Natalia: Si, stiamo lavorando su delle pubblicazioni che sono già disponibili all’interno delle nostre Unviersità e ovviamente sul progetto congiunto COVID.SI/SIDOCK, per il quale ci aspettiamo che la prima pubblicazione relativa ai risultati in silico (simulati al computer) sia disponibile per il 21. In un anno, speriamo di avere composti sperimentali di successo, collaborazione in biologia e una comunità consolidata in cui possiamo lavorare insieme per affrontare e comunicare i problemi della progettazione di farmaci.

Matteo: I risultati saranno pubblicati come open science?

Marko & Natalia: Assolutamente, vogliamo contribuire anche all’OpenScience. Speriamo di aver risposto alle tue domande e ringrazio te e tutti i partecipanti per il vostro supporto. Ci auguriamo di poter lavorare ancora di più nel prossimo futuro.

There is only a tiny part that wasn't too clear to me, it's marked by NDT in the translation (NDT in Italian means "Nota del traduttore", ie, "annotation of the translator")
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Message 251 - Posted: 11 Dec 2020, 23:12:56 UTC - in response to Message 239.  
Last modified: 11 Dec 2020, 23:21:08 UTC

We even have here a Russian enthusiast who can make translations to Italian and will love to, and you could be our expert and check :)

Yes of course! I wish him all the luck for his study of Italian :)

Moreover, I'd like to signal you also another interesting Boinc project that is working on Coronavirus, perhaps you already know it, it's Tn-Grid https://gene.disi.unitn.it/test. I published a post on the forum of the Postera project some times ago https://discuss.postera.ai/t/expansion-of-gene-networks-related-to-covid/1753, I don't know, perhaps it could be useful in some way, I like to do my tiny tiny tiny part in connecting scientists.

Hi all, not a scientist myself, so my contribution in this forum will be limited to this topic. I am a distributed computer volunteer, and I knew Postera thanks to the Folding@Home forum.
I’d like to signal to you another project which worked on Sars-Cov2 and as far as I know their work on the virus is completed. It’s called Tn-Grid and they performed the “expansion of gene regulatory network” (I don’t know what it is) on all the genes believed to be related to the virus. Some of these genes are:
ACE2 AGT AGTR1 AGTR2 REN MME DPP4 PRCP MEP1B MEP1A XPNPEP2 MME DPP4 BRD2 INS GIP SLC5A2 SLC5A5 ADA GCG GLP1R PTPRC CD28 CCR7 PDCD1 SNCA SPATA2 CD27 B3GAT1 IL7 IL2RA ISG20 FAS PTPN13 CD38 CD74 CD24 CR2
the total number is 1242
If someone of you think it can be of any help, I think you should contact them. They are a group of researcher at Università di Trento, Italy.

Post about covid: https://gene.disi.unitn.it/test/forum_thread.php?id=265
Website: https://gene.disi.unitn.it/test

Answer:

Thanks for the post here; I for one wasn’t aware of the their work. It seems their work becomes very useful when deciding which target or biological pathway to select for then developing a therapy to combat SARS-COV-2. In Moonshot’s case, all our work has been focused on a single target – inhibiting the main protease, a key enzyme involved in viral replication, and our emphasis right now is on experimental testing of compounds rather than looking for new targets. But we’ll certainly bear their work in mind.


To sum up, distributed computing projects that are workin/worked on Covid are:
- Rosetta@Home (de novo protein design of covid inhibitor, prediction of 3d shape of protein from the sequence of aminoacids and so on)
- Folding@Home, and the related Postera project
- World Community Grid - OPN1
- Boinc@Tacc (some related with autodock)
- Ibercivis 2 (some autodock too)
- TN-Grid Gene@Home: Expansion of gene networks related to Covid[/quote]
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Message 253 - Posted: 12 Dec 2020, 11:08:58 UTC - in response to Message 250.  

Wow, thank you very much for the work! :) We feel proud that many people are interested in the project and its science!
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Message 254 - Posted: 12 Dec 2020, 16:39:27 UTC - in response to Message 250.  

https://covid.si/en/intervista-riguardo-il-progetto-boinc-sidockhome/
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