Folding project #17308, COVID-19 research

Research section Research projects and references

Project #17308 overview

Project Summary AI Beta

This project studies how the SARS-CoV-2 virus attaches to human cells. Scientists are using computer simulations to understand how proteins on the virus and in our bodies interact. They hope this will lead to better 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: 158,384
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

Scientific: Biotechnology, HealthcareVirology / Infectious Diseases

SARS-CoV-2 is the virus that causes COVID-19. It's a type of coronavirus, which are common viruses that can cause illnesses ranging from the common cold to more severe diseases like SARS and MERS.

Receptor binding domain (RBD)

Region of the SARS-CoV-2 spike protein that binds to host cell receptors

Scientific: Biotechnology, HealthcareVirology / Structural Biology

The receptor binding domain (RBD) is a part of the spike protein found on the surface of the SARS-CoV-2 virus. This domain is responsible for attaching the virus to human cells, allowing it to infect them.

ACE2

Angiotensin-converting enzyme 2

Scientific: Biotechnology, HealthcareVirology / Cellular Biology

ACE2 is a protein found on the surface of human cells. The SARS-CoV-2 virus uses ACE2 as its entry point into human cells.

Glycosylation

The process of adding sugar molecules to proteins

Scientific: Biotechnology, PharmaceuticalsBiochemistry / Protein Modification

Glycosylation is a common process in which sugar molecules are attached to proteins. This process can affect the function and stability of proteins.

Markov State Models

Mathematical models used to simulate the dynamics of complex systems

Scientific: Biotechnology, PharmaceuticalsBiophysics / Computational Biology

Markov state models are a powerful tool for studying the behavior of complex systems over time. They can be used to predict how systems will evolve and to understand the underlying mechanisms that govern their behavior.

Metastable states

States that are relatively stable but can transition to other states over time

Scientific: Biotechnology, PharmaceuticalsBiophysics / Molecular Dynamics

Metastable states are temporary configurations that molecules can exist in. These states are more stable than highly unstable configurations, but they can eventually transform into a different state.

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	6,544,556	206,338	31.72	0 ^hrs 45 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	4,808,498	186,780	25.74	0 ^hrs 56 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,772,519	188,195	25.36	0 ^hrs 57 ^mins
4	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,683,709	186,456	25.12	0 ^hrs 57 ^mins
5	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	3,776,453	173,824	21.73	1 ^hrs 6 ^mins
6	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,448,598	169,583	20.34	1 ^hrs 11 ^mins
7	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,377,624	165,817	20.37	1 ^hrs 11 ^mins
8	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	3,030,425	161,875	18.72	1 ^hrs 17 ^mins
9	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,913,214	160,228	18.18	1 ^hrs 19 ^mins
10	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,780,461	157,837	17.62	1 ^hrs 22 ^mins
11	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER]	Nvidia	TU104	2,604,085	154,400	16.87	1 ^hrs 25 ^mins
12	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,593,172	148,060	17.51	1 ^hrs 22 ^mins
13	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,393,815	146,694	16.32	1 ^hrs 28 ^mins
14	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,165,141	144,667	14.97	1 ^hrs 36 ^mins
15	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,094,564	142,736	14.67	1 ^hrs 38 ^mins
16	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,053,146	141,467	14.51	1 ^hrs 39 ^mins
17	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	1,980,316	140,895	14.06	1 ^hrs 42 ^mins
18	GeForce RTX 2060 KO TU106-200A [GeForce RTX 2060]	Nvidia	TU106-200A	1,873,830	138,475	13.53	1 ^hrs 46 ^mins
19	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,841,485	137,211	13.42	1 ^hrs 47 ^mins

20	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,693,732	133,918	12.65	1 ^hrs 54 ^mins
21	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	1,662,263	131,479	12.64	1 ^hrs 54 ^mins
22	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,591,970	130,587	12.19	1 ^hrs 58 ^mins
23	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	1,512,889	128,861	11.74	2 ^hrs 3 ^mins
24	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,472,020	126,058	11.68	2 ^hrs 3 ^mins
25	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,307,670	122,276	10.69	2 ^hrs 15 ^mins
26	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,189,615	117,869	10.09	2 ^hrs 23 ^mins
27	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,135,260	116,821	9.72	2 ^hrs 28 ^mins
28	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,125,021	116,260	9.68	2 ^hrs 29 ^mins
29	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,022,859	112,682	9.08	2 ^hrs 39 ^mins
30	Radeon RX 5600/5600 XT - 5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT / 5700/5700 XT]	AMD	Navi 10	920,009	108,296	8.50	2 ^hrs 50 ^mins
31	GeForce RTX 2060 Mobile / Max-Q TU106M [GeForce RTX 2060 Mobile / Max-Q] 4550	Nvidia	TU106M	886,159	107,310	8.26	2 ^hrs 54 ^mins
32	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	857,734	106,896	8.02	2 ^hrs 59 ^mins
33	P104-100 GP104 [P104-100]	Nvidia	GP104	681,532	98,839	6.90	3 ^hrs 29 ^mins
34	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	672,165	98,102	6.85	3 ^hrs 30 ^mins
35	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	634,613	94,349	6.73	3 ^hrs 34 ^mins
36	GeForce GTX 1650 SUPER TU116 [GeForce GTX 1650 SUPER]	Nvidia	TU116	577,286	93,584	6.17	3 ^hrs 53 ^mins
37	Quadro P2200 GP106GL [Quadro P2200]	Nvidia	GP106GL	504,105	89,333	5.64	4 ^hrs 15 ^mins
38	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	479,822	87,720	5.47	4 ^hrs 23 ^mins
39	P106-100 GP106 [P106-100]	Nvidia	GP106	471,532	87,487	5.39	4 ^hrs 27 ^mins

40	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	457,165	86,548	5.28	4 ^hrs 33 ^mins
41	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	442,217	85,416	5.18	4 ^hrs 38 ^mins
42	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	417,159	83,549	4.99	4 ^hrs 48 ^mins
43	GeForce GTX 1050 Ti GP107 [GeForce GTX 1050 Ti] 2138	Nvidia	GP107	382,378	81,512	4.69	5 ^hrs 7 ^mins
44	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	330,280	75,739	4.36	5 ^hrs 30 ^mins
45	P106-090 GP106 [P106-090]	Nvidia	GP106	311,326	76,162	4.09	5 ^hrs 52 ^mins
46	Quadro T1000 Mobile TU117GLM [Quadro T1000 Mobile]	Nvidia	TU117GLM	282,318	73,840	3.82	6 ^hrs 17 ^mins
47	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	231,157	67,787	3.41	7 ^hrs 2 ^mins
48	Radeon RX 460 Baffin XT [Radeon RX 460]	AMD	Baffin XT	162,083	61,531	2.63	9 ^hrs 7 ^mins
49	Radeon R9 200 Series Hawaii [Radeon R9 200 Series]	AMD	Hawaii	157,050	60,458	2.60	9 ^hrs 14 ^mins
50	Polaris11 Baffin [Polaris11]	AMD	Baffin	139,365	58,313	2.39	10 ^hrs 3 ^mins
51	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	134,039	57,507	2.33	10 ^hrs 18 ^mins
52	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	126,286	54,177	2.33	10 ^hrs 18 ^mins
53	Radeon RX Vega gfx902 raven [Radeon RX Vega gfx902]	AMD	raven	27,491	33,949	0.81	29 ^hrs 38 ^mins

Research: COVID-19 Folding Project #17308

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17308

GPU PPD Averages

Research: COVID-19 Folding Project #17308

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages