Folding project #17309, COVID-19 research

Research section Research projects and references

Project #17309 overview

Project Summary AI Beta

This project studies how the SARS-CoV-2 spike protein binds to human cells. By simulating these proteins, researchers want to understand how sugar molecules on the virus affect its shape and binding ability. This knowledge could help develop new drugs against 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: 200,474
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: these projects are replacing 17304-6, as 17304-6 had to be stopped due to work server issues.

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 / Virology

SARS-CoV-2 is a virus that causes COVID-19. It is a type of coronavirus that spreads easily from person to person through respiratory droplets.

receptor binding domain (RBD)

Receptor Binding Domain

Protein Domain: Pharmaceutical ResearchBiotechnology / Structural Biology

The receptor binding domain (RBD) is a part of the spike protein on SARS-CoV-2 that binds to the ACE2 receptor on human cells, allowing the virus to infect.

ACE2

Angiotensin-converting enzyme 2

Protein: Pharmaceutical ResearchBiotechnology / 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. The SARS-CoV-2 virus uses ACE2 as its entry point into human cells.

glycosylation

The addition of sugar molecules to proteins or other biomolecules.

Biochemical Modification: Pharmaceutical ResearchBiotechnology / Molecular Biology

Glycosylation is a process where sugar molecules are attached to proteins. This can affect how proteins fold, interact with other molecules, and function.

Markov State Models

Mathematical models used to describe the probabilistic transitions between different states of a system.

Computational Model: Drug DiscoveryBioinformatics / Molecular Dynamics

Markov State Models are computer simulations that help us understand how molecules move and change over time. They are used in drug discovery to study protein interactions and design new drugs.

metastable states

Stable but transient states of a system that can persist for a certain amount of time before transitioning to another state.

Scientific Concept: Pharmaceutical ResearchBiochemistry / Protein Structure

Metastable states are like temporary resting places that molecules can occupy. Understanding these states is important for drug design because it can help us predict how proteins will behave when bound to a drug.

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	5,843,378	257,840	22.66	1 ^hrs 4 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	4,630,357	237,945	19.46	1 ^hrs 14 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,191,547	231,577	18.10	1 ^hrs 20 ^mins
4	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,116,212	230,351	17.87	1 ^hrs 21 ^mins
5	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	3,555,393	219,487	16.20	1 ^hrs 29 ^mins
6	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	3,407,324	215,015	15.85	1 ^hrs 31 ^mins
7	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	2,962,150	204,735	14.47	1 ^hrs 40 ^mins
8	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	2,825,050	207,749	13.60	1 ^hrs 46 ^mins
9	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,748,720	201,980	13.61	1 ^hrs 46 ^mins
10	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,639,018	198,926	13.27	1 ^hrs 49 ^mins
11	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,559,277	193,981	13.19	1 ^hrs 49 ^mins
12	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,524,025	195,999	12.88	1 ^hrs 52 ^mins
13	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,485,843	195,627	12.71	1 ^hrs 53 ^mins
14	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,324,764	189,006	12.30	1 ^hrs 57 ^mins
15	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER]	Nvidia	TU104	2,290,391	190,367	12.03	1 ^hrs 60 ^mins
16	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,027,259	181,808	11.15	2 ^hrs 9 ^mins
17	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	1,967,969	179,626	10.96	2 ^hrs 11 ^mins
18	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	1,836,907	175,162	10.49	2 ^hrs 17 ^mins
19	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	1,792,566	175,501	10.21	2 ^hrs 21 ^mins

20	GeForce RTX 2070 Mobile TU106BM [GeForce RTX 2070 Mobile] 6636	Nvidia	TU106BM	1,767,446	174,889	10.11	2 ^hrs 22 ^mins
21	GeForce RTX 2060 KO TU106-200A [GeForce RTX 2060]	Nvidia	TU106-200A	1,677,667	171,709	9.77	2 ^hrs 27 ^mins
22	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	1,578,537	163,958	9.63	2 ^hrs 30 ^mins
23	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,564,605	166,826	9.38	2 ^hrs 34 ^mins
24	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,560,219	166,280	9.38	2 ^hrs 33 ^mins
25	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	1,546,769	164,568	9.40	2 ^hrs 33 ^mins
26	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,474,838	163,420	9.02	2 ^hrs 40 ^mins
27	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,223,663	154,428	7.92	3 ^hrs 2 ^mins
28	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,208,707	151,770	7.96	3 ^hrs 1 ^mins
29	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,133,879	149,855	7.57	3 ^hrs 10 ^mins
30	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,070,506	146,777	7.29	3 ^hrs 17 ^mins
31	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,032,221	144,364	7.15	3 ^hrs 21 ^mins
32	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,029,245	145,651	7.07	3 ^hrs 24 ^mins
33	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	954,206	141,011	6.77	3 ^hrs 33 ^mins
34	Radeon RX 5600/5600 XT - 5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT / 5700/5700 XT]	AMD	Navi 10	951,636	140,822	6.76	3 ^hrs 33 ^mins
35	GeForce RTX 2060 Mobile / Max-Q TU106M [GeForce RTX 2060 Mobile / Max-Q] 4550	Nvidia	TU106M	936,309	139,598	6.71	3 ^hrs 35 ^mins
36	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	893,282	138,631	6.44	3 ^hrs 43 ^mins
37	Radeon RX 5600 OEM/5600 XT/5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT/5700/5700 XT]	AMD	Navi 10	842,917	127,580	6.61	3 ^hrs 38 ^mins
38	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	685,187	122,402	5.60	4 ^hrs 17 ^mins
39	P104-100 GP104 [P104-100]	Nvidia	GP104	639,114	124,449	5.14	4 ^hrs 40 ^mins

40	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	632,670	122,645	5.16	4 ^hrs 39 ^mins
41	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	607,211	121,623	4.99	4 ^hrs 48 ^mins
42	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	586,369	119,790	4.89	4 ^hrs 54 ^mins
43	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	540,686	117,646	4.60	5 ^hrs 13 ^mins
44	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	528,008	115,384	4.58	5 ^hrs 15 ^mins
45	GeForce GTX 1650 SUPER TU116 [GeForce GTX 1650 SUPER]	Nvidia	TU116	512,448	114,598	4.47	5 ^hrs 22 ^mins
46	P106-100 GP106 [P106-100]	Nvidia	GP106	449,138	110,462	4.07	5 ^hrs 54 ^mins
47	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	441,909	109,973	4.02	5 ^hrs 58 ^mins
48	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	438,988	107,675	4.08	5 ^hrs 53 ^mins
49	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	434,725	108,742	4.00	6 ^hrs 0 ^mins
50	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	413,920	107,263	3.86	6 ^hrs 13 ^mins
51	Quadro P2200 GP106GL [Quadro P2200]	Nvidia	GP106GL	395,613	104,735	3.78	6 ^hrs 21 ^mins
52	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	390,848	105,756	3.70	6 ^hrs 30 ^mins
53	GeForce GTX 1050 Ti GP107 [GeForce GTX 1050 Ti] 2138	Nvidia	GP107	338,240	100,656	3.36	7 ^hrs 9 ^mins
54	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	320,912	96,811	3.31	7 ^hrs 14 ^mins
55	P106-090 GP106 [P106-090]	Nvidia	GP106	270,232	93,374	2.89	8 ^hrs 18 ^mins
56	Quadro T1000 Mobile TU117GLM [Quadro T1000 Mobile]	Nvidia	TU117GLM	266,824	93,074	2.87	8 ^hrs 22 ^mins
57	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	263,674	92,774	2.84	8 ^hrs 27 ^mins
58	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	207,567	82,005	2.53	9 ^hrs 29 ^mins
59	Radeon RX 460 Baffin XT [Radeon RX 460]	AMD	Baffin XT	163,542	79,250	2.06	11 ^hrs 38 ^mins

60	Radeon R9 200 Series Hawaii [Radeon R9 200 Series]	AMD	Hawaii	151,422	76,600	1.98	12 ^hrs 8 ^mins
61	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	136,679	74,371	1.84	13 ^hrs 4 ^mins
62	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	104,968	55,862	1.88	12 ^hrs 46 ^mins
63	Radeon HD 7790 Bonaire XT [Radeon HD 7790]	AMD	Bonaire XT	102,861	65,826	1.56	15 ^hrs 22 ^mins
64	Polaris11 Baffin [Polaris11]	AMD	Baffin	93,529	64,594	1.45	16 ^hrs 35 ^mins
65	Radeon R7 250X/HD 7700/8760 R575A [Radeon R7 250X/HD 7700/8760]	AMD	R575A	65,971	58,226	1.13	21 ^hrs 11 ^mins
66	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	46,353	51,452	0.90	26 ^hrs 38 ^mins
67	Radeon RX Vega gfx902 raven [Radeon RX Vega gfx902]	AMD	raven	27,339	43,489	0.63	38 ^hrs 11 ^mins

Research: COVID-19 Folding Project #17309

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17309

GPU PPD Averages

Research: COVID-19 Folding Project #17309

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages