Folding project #17319, COVID-19 research

Research section Research projects and references

Project #17319 overview

Project Summary AI Beta

This project uses computer simulations to study how the SARS-CoV-2 virus attaches to human cells. Researchers are looking at how sugar molecules (glycosylation) affect the shape of the virus and its ability to bind to a protein called ACE2 on our cells. Understanding this could help scientists develop new drugs to fight COVID-19.

Automated summary; simplified and may not be fully accurate.

Project team

Manager(s): Ivy Zhang
Institution: Memorial Sloan Kettering Cancer Center
Website: Open project site

Work unit

Atoms: 284,612
Core: OPENMM_22
Status: Public

Source material

Official Project Description

These projects involve the SARS-CoV-2 receptor binding domain (RBD) and its target receptor in humans, ACE2.

We are simulating these proteins alone and in complex with each other (and with and without glycosylation).

We will build Markov State Models using the Fah simulation data, which will help us identify the metastable states of each protein/protein complex.

Given these experiments, we hope to be able to explain the impact of glycosylation on RBD conformational dynamics as well as identify whether there are shifts in metastable states upon RBD:ACE2 binding.

Ultimately, the knowledge gained here will help infom drug design efforts. Note: 17313-6 replace 17307-9, as 17307-9 used a different, less stable integrator.

Reading reference

Related Terms Glossary AI Beta

Automated high-level definitions; simplified and may not be fully accurate.

SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2

Virus: BiotechnologyInfectious Disease / Viral Immunology

SARS-CoV-2 is the virus responsible for causing COVID-19. It's a type of coronavirus that primarily affects the respiratory system.

Receptor Binding Domain (RBD)

Region of the SARS-CoV-2 spike protein that binds to ACE2 receptors.

Protein Region: BiotechnologyInfectious Disease / Structural Biology

The RBD is a crucial part of the SARS-CoV-2 virus. It allows the virus to attach itself to human cells by binding to the ACE2 receptor.

ACE2

Angiotensin-converting enzyme 2

Protein: BiotechnologyInfectious Disease / Cellular Biology

ACE2 is a protein found on the surface of many human cells. It plays a role in regulating blood pressure and other bodily functions.

Glycosylation

The process of adding sugar molecules to proteins.

Cellular Process: PharmaceuticalBiochemistry / Protein Modification

Glycosylation is a common modification of proteins that can affect their structure, function, and interactions with other molecules.

Markov State Models

Mathematical models used to predict the future behavior of complex systems.

Computational Tool: BiotechnologyBiophysics / Molecular Dynamics Simulation

Markov State Models are a powerful tool for understanding how molecules move and interact over time. They can be used to simulate protein folding, drug binding, and other biological processes.

Metastable States

Transient states that a system can exist in before transitioning to another state.

Scientific Concept: PharmaceuticalBiophysics / Molecular Dynamics Simulation

Metastable states are like temporary resting points for molecules. Understanding these states can help us predict how proteins will behave and interact.

Drug Design

The process of designing and developing new medications.

Scientific Process: PharmaceuticalPharmaceutical / Medicinal Chemistry

Drug design is a complex process that involves identifying potential drug targets, screening for promising compounds, and optimizing their properties.

GPU PPD Averages

Rank Project	Model Name Folding@Home Identifier	Make Brand	GPU Model	PPD Average	Points WU Average	WUs Day Average	WU Time Average
1	GeForce RTX 3090 GA102 [GeForce RTX 3090]	Nvidia	GA102	7,002,217	491,137	14.26	1 ^hrs 41 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,745,916	462,363	12.43	1 ^hrs 56 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,921,158	438,507	11.22	2 ^hrs 8 ^mins
4	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	4,514,416	424,342	10.64	2 ^hrs 15 ^mins
5	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,429,246	423,571	10.46	2 ^hrs 18 ^mins
6	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	4,063,171	411,669	9.87	2 ^hrs 26 ^mins
7	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,938,758	407,352	9.67	2 ^hrs 29 ^mins
8	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,429,354	388,045	8.84	2 ^hrs 43 ^mins
9	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,902,897	368,763	7.87	3 ^hrs 3 ^mins
10	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,841,743	362,538	7.84	3 ^hrs 4 ^mins
11	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,829,020	358,162	7.90	3 ^hrs 2 ^mins
12	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	2,737,124	358,818	7.63	3 ^hrs 9 ^mins
13	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,615,607	350,160	7.47	3 ^hrs 13 ^mins
14	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,599,711	351,626	7.39	3 ^hrs 15 ^mins
15	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,515,403	351,027	7.17	3 ^hrs 21 ^mins
16	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,408,033	345,329	6.97	3 ^hrs 27 ^mins
17	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	2,322,788	333,283	6.97	3 ^hrs 27 ^mins
18	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,245,571	336,477	6.67	3 ^hrs 36 ^mins
19	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,228,738	335,057	6.65	3 ^hrs 36 ^mins

20	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,089,663	321,470	6.50	3 ^hrs 42 ^mins
21	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,831,777	315,297	5.81	4 ^hrs 8 ^mins
22	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,705,016	308,511	5.53	4 ^hrs 21 ^mins
23	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,623,894	302,842	5.36	4 ^hrs 29 ^mins
24	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,429,068	291,182	4.91	4 ^hrs 53 ^mins
25	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,403,756	287,827	4.88	4 ^hrs 55 ^mins
26	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,335,965	281,908	4.74	5 ^hrs 4 ^mins
27	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,305,896	280,531	4.66	5 ^hrs 9 ^mins
28	GeForce RTX 2060 Mobile / Max-Q TU106M [GeForce RTX 2060 Mobile / Max-Q] 4550	Nvidia	TU106M	1,287,176	281,070	4.58	5 ^hrs 14 ^mins
29	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,239,429	273,219	4.54	5 ^hrs 17 ^mins
30	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,205,910	274,005	4.40	5 ^hrs 27 ^mins
31	Radeon RX 5600 OEM/5600 XT/5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT/5700/5700 XT]	AMD	Navi 10	1,151,306	265,138	4.34	5 ^hrs 32 ^mins
32	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,120,660	265,573	4.22	5 ^hrs 41 ^mins
33	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,106,880	262,770	4.21	5 ^hrs 42 ^mins
34	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,099,688	265,587	4.14	5 ^hrs 48 ^mins
35	Tesla M40 GM200GL [Tesla M40] 6844	Nvidia	GM200GL	963,413	255,675	3.77	6 ^hrs 22 ^mins
36	P104-100 GP104 [P104-100]	Nvidia	GP104	938,008	253,062	3.71	6 ^hrs 28 ^mins
37	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	836,822	242,388	3.45	6 ^hrs 57 ^mins
38	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	703,448	229,087	3.07	7 ^hrs 49 ^mins
39	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	696,709	221,099	3.15	7 ^hrs 37 ^mins

40	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	693,120	227,843	3.04	7 ^hrs 53 ^mins
41	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	639,584	222,489	2.87	8 ^hrs 21 ^mins
42	P106-100 GP106 [P106-100]	Nvidia	GP106	604,474	218,370	2.77	8 ^hrs 40 ^mins
43	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	583,536	215,005	2.71	8 ^hrs 51 ^mins
44	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	533,400	209,876	2.54	9 ^hrs 27 ^mins
45	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	531,613	197,021	2.70	8 ^hrs 54 ^mins
46	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	506,331	205,431	2.46	9 ^hrs 44 ^mins
47	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	468,523	201,183	2.33	10 ^hrs 18 ^mins
48	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	463,959	200,023	2.32	10 ^hrs 21 ^mins
49	Quadro T2000 Mobile / Max-Q TU117GLM [Quadro T2000 Mobile / Max-Q]	Nvidia	TU117GLM	441,608	190,528	2.32	10 ^hrs 21 ^mins
50	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	406,289	186,501	2.18	11 ^hrs 1 ^mins
51	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	337,360	179,899	1.88	12 ^hrs 48 ^mins
52	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	306,118	174,543	1.75	13 ^hrs 41 ^mins
53	P106-090 GP106 [P106-090]	Nvidia	GP106	292,618	171,581	1.71	14 ^hrs 4 ^mins
54	Radeon R9 200/300 Series Tonga [Radeon R9 200/300 Series]	AMD	Tonga	275,995	168,263	1.64	14 ^hrs 38 ^mins
55	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	189,818	138,512	1.37	17 ^hrs 31 ^mins
56	GeForce GTX 1660 Mobile TU116M [GeForce GTX 1660 Mobile]	Nvidia	TU116M	80,152	111,801	0.72	33 ^hrs 29 ^mins
57	Radeon R7/R6 360 Series Bonaire [Radeon R7/R6 360 Series]	AMD	Bonaire	75,448	104,517	0.72	33 ^hrs 15 ^mins
58	Radeon R7 250X/HD 7700/8760 R575A [Radeon R7 250X/HD 7700/8760]	AMD	R575A	73,376	108,451	0.68	35 ^hrs 28 ^mins
59	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	52,595	96,801	0.54	44 ^hrs 10 ^mins

60	Radeon APU A4-6000 R2 Mullins [Radeon APU A4-6000 R2]	AMD	Mullins	43,960	87,920	0.50	48 ^hrs 0 ^mins
61	Radeon R7 250/HD 7700 R575A [Radeon R7 250/HD 7700]	AMD	R575A	43,907	88,270	0.50	48 ^hrs 15 ^mins

Research: COVID-19 Folding Project #17319

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17319

GPU PPD Averages

Research: COVID-19 Folding Project #17319

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages