Folding project #17316, COVID-19 research

Research section Research projects and references

Project #17316 overview

Project Summary AI Beta

This project studies how the spike protein from the virus that causes COVID-19 (SARS-CoV-2) binds to human cells. By simulating these proteins, scientists hope to understand how sugar molecules on the spike protein affect its shape and binding ability. This knowledge could help in developing 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: 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: 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

Scientific: Biotechnology, MedicineVirology / Coronavirus Research

SARS-CoV-2 is the virus that causes COVID-19. It's a type of coronavirus that spreads easily from person to person through respiratory droplets. Understanding SARS-CoV-2 is crucial for developing treatments and vaccines.

RBD

Receptor binding domain

Scientific: Biotechnology, MedicineVirology / Protein Structure

The receptor-binding domain (RBD) is a part of the SARS-CoV-2 spike protein that allows the virus to attach to and enter human cells. Drugs targeting RBD can prevent infection.

ACE2

Angiotensin-converting enzyme 2

Scientific: Biotechnology, MedicinePhysiology / Cellular Receptors

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

Glycosylation

The process of adding sugar molecules to proteins

Scientific: Biotechnology, MedicineBiochemistry / Protein Modification

Glycosylation is a common modification of proteins that can affect their function. In the case of SARS-CoV-2, glycosylation on the RBD protein may influence its ability to bind to ACE2.

Markov State Models

Mathematical models used to simulate the behavior of complex systems over time

Scientific: Biotechnology, MedicineComputational Biology / Molecular Dynamics

Markov State Models are used in computational biology to study the dynamics of proteins and other molecules. They can help predict how a protein will fold or how it will interact with other molecules.

Metastable States

Temporary states that are relatively stable but can transition to other states

Scientific: Biotechnology, MedicineChemistry / Physical Chemistry

Metastable states are important in understanding the behavior of molecules. In the case of proteins, metastable states can represent different conformations that the protein can adopt.

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	6,345,226	339,337	18.70	1 ^hrs 17 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,078,293	315,532	16.09	1 ^hrs 29 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,593,519	308,001	14.91	1 ^hrs 37 ^mins
4	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,344,529	301,642	14.40	1 ^hrs 40 ^mins
5	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	4,292,144	303,992	14.12	1 ^hrs 42 ^mins
6	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	3,865,512	289,910	13.33	1 ^hrs 48 ^mins
7	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,319,791	275,197	12.06	1 ^hrs 59 ^mins
8	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,125,047	270,495	11.55	2 ^hrs 5 ^mins
9	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,848,414	263,162	10.82	2 ^hrs 13 ^mins
10	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,792,587	259,745	10.75	2 ^hrs 14 ^mins
11	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	2,642,947	254,341	10.39	2 ^hrs 19 ^mins
12	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,584,492	252,631	10.23	2 ^hrs 21 ^mins
13	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	2,437,392	248,435	9.81	2 ^hrs 27 ^mins
14	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,418,917	246,388	9.82	2 ^hrs 27 ^mins
15	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,413,493	248,262	9.72	2 ^hrs 28 ^mins
16	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,330,434	227,245	10.26	2 ^hrs 20 ^mins
17	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,257,907	241,635	9.34	2 ^hrs 34 ^mins
18	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,227,137	240,240	9.27	2 ^hrs 35 ^mins
19	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER]	Nvidia	TU104	2,148,526	238,635	9.00	2 ^hrs 40 ^mins

20	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,102,577	235,748	8.92	2 ^hrs 41 ^mins
21	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,012,123	231,829	8.68	2 ^hrs 46 ^mins
22	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,644,603	216,955	7.58	3 ^hrs 10 ^mins
23	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,589,189	215,576	7.37	3 ^hrs 15 ^mins
24	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,498,999	210,727	7.11	3 ^hrs 22 ^mins
25	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,358,216	205,064	6.62	3 ^hrs 37 ^mins
26	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,276,343	200,377	6.37	3 ^hrs 46 ^mins
27	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,265,831	196,700	6.44	3 ^hrs 44 ^mins
28	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,213,478	196,897	6.16	3 ^hrs 54 ^mins
29	GeForce RTX 2060 Mobile / Max-Q TU106M [GeForce RTX 2060 Mobile / Max-Q] 4550	Nvidia	TU106M	1,137,168	193,539	5.88	4 ^hrs 5 ^mins
30	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,132,582	191,777	5.91	4 ^hrs 4 ^mins
31	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,070,176	189,074	5.66	4 ^hrs 14 ^mins
32	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,068,194	179,753	5.94	4 ^hrs 2 ^mins
33	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,053,487	186,130	5.66	4 ^hrs 14 ^mins
34	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,044,197	187,408	5.57	4 ^hrs 18 ^mins
35	Radeon RX 5600 OEM/5600 XT/5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT/5700/5700 XT]	AMD	Navi 10	1,039,742	186,146	5.59	4 ^hrs 18 ^mins
36	Tesla M40 GM200GL [Tesla M40] 6844	Nvidia	GM200GL	932,288	171,466	5.44	4 ^hrs 25 ^mins
37	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	891,455	178,506	4.99	4 ^hrs 48 ^mins
38	P104-100 GP104 [P104-100]	Nvidia	GP104	764,075	169,501	4.51	5 ^hrs 19 ^mins
39	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	689,995	161,906	4.26	5 ^hrs 38 ^mins

40	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	667,993	160,495	4.16	5 ^hrs 46 ^mins
41	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	637,844	159,107	4.01	5 ^hrs 59 ^mins
42	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	617,975	157,701	3.92	6 ^hrs 7 ^mins
43	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	615,614	157,161	3.92	6 ^hrs 8 ^mins
44	GeForce GTX 1650 SUPER TU116 [GeForce GTX 1650 SUPER]	Nvidia	TU116	578,609	146,958	3.94	6 ^hrs 6 ^mins
45	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	553,515	151,354	3.66	6 ^hrs 34 ^mins
46	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	516,109	145,878	3.54	6 ^hrs 47 ^mins
47	P106-100 GP106 [P106-100]	Nvidia	GP106	504,816	147,696	3.42	7 ^hrs 1 ^mins
48	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	437,679	140,486	3.12	7 ^hrs 42 ^mins
49	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	436,338	140,338	3.11	7 ^hrs 43 ^mins
50	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	431,053	140,346	3.07	7 ^hrs 49 ^mins
51	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	385,982	118,120	3.27	7 ^hrs 21 ^mins
52	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	326,763	127,757	2.56	9 ^hrs 23 ^mins
53	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	285,180	121,749	2.34	10 ^hrs 15 ^mins
54	P106-090 GP106 [P106-090]	Nvidia	GP106	270,379	119,869	2.26	10 ^hrs 38 ^mins
55	Radeon R9 200/300 Series Tonga [Radeon R9 200/300 Series]	AMD	Tonga	246,064	114,792	2.14	11 ^hrs 12 ^mins
56	Quadro T2000 Mobile / Max-Q TU117GLM [Quadro T2000 Mobile / Max-Q]	Nvidia	TU117GLM	229,536	141,295	1.62	14 ^hrs 46 ^mins
57	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	204,072	109,066	1.87	12 ^hrs 50 ^mins
58	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	173,278	103,110	1.68	14 ^hrs 17 ^mins
59	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	163,997	85,339	1.92	12 ^hrs 29 ^mins

60	Radeon HD 7790 Bonaire XT [Radeon HD 7790]	AMD	Bonaire XT	98,739	73,712	1.34	17 ^hrs 55 ^mins
61	Radeon R7/R6 360 Series Bonaire [Radeon R7/R6 360 Series]	AMD	Bonaire	73,319	76,713	0.96	25 ^hrs 7 ^mins
62	Radeon RX Vega gfx902 raven [Radeon RX Vega gfx902]	AMD	raven	72,653	77,391	0.94	25 ^hrs 34 ^mins
63	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	51,561	68,996	0.75	32 ^hrs 7 ^mins
64	Ryzen 4900HS mobile Renoir [Ryzen 4900HS mobile]	AMD	Renoir	31,541	58,251	0.54	44 ^hrs 19 ^mins

Research: COVID-19 Folding Project #17316

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17316

GPU PPD Averages

Research: COVID-19 Folding Project #17316

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages