Folding project #17320, COVID-19 research

Research section Research projects and references

Project #17320 overview

Project Summary AI Beta

This project studies how the SARS-CoV-2 virus attaches to human cells. Researchers are simulating proteins involved in this attachment and how sugar molecules affect their shape. By understanding these interactions, they hope to 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: 330,617
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 Pathogenesis

SARS-CoV-2 is the virus responsible for causing COVID-19. It's a type of coronavirus that affects the respiratory system, leading to symptoms like fever, cough, and difficulty breathing.

RBD

Receptor binding domain

Protein Domain: BiotechnologyMolecular Biology / Structural Biology

The RBD is a part of the SARS-CoV-2 spike protein that binds to the ACE2 receptor on human cells. This binding allows the virus to enter and infect cells.

ACE2

Angiotensin-converting enzyme 2

Protein Receptor: BiotechnologyCellular Biology / Signal Transduction

ACE2 is a protein found on the surface of many human cells. The SARS-CoV-2 virus uses ACE2 as a doorway to enter and infect these cells.

Glycosylation

The process of adding sugar molecules to proteins.

Biochemical Modification: BiotechnologyMolecular Biology / Protein Chemistry

Glycosylation is a common modification of proteins that can affect their function and interactions. In the case of SARS-CoV-2, glycosylation can influence how well the virus binds to human cells.

Markov State Models

A type of computational model used to study the dynamics of complex systems.

Computational Method: BiotechnologyBioinformatics / Molecular Dynamics Simulation

Markov State Models are used in bioinformatics to simulate the movement and interactions of molecules over time. This can help researchers understand how proteins fold, interact with each other, and carry out their functions.

Metastable States

States of a system that are stable for a certain period of time but can transition to other states.

Physical Property: BiotechnologyBiophysics / Protein Folding

Proteins exist in different metastable states as they fold and interact. Understanding these states can provide insights into protein function and how diseases like COVID-19 arise.

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	6,906,551	607,496	11.37	2 ^hrs 7 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,593,632	566,770	9.87	2 ^hrs 26 ^mins
3	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	4,834,171	534,896	9.04	2 ^hrs 39 ^mins
4	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,725,588	541,585	8.73	2 ^hrs 45 ^mins
5	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,472,676	530,642	8.43	2 ^hrs 51 ^mins
6	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	4,052,765	512,229	7.91	3 ^hrs 2 ^mins
7	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,726,577	502,572	7.42	3 ^hrs 14 ^mins
8	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,327,015	476,569	6.98	3 ^hrs 26 ^mins
9	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,994,339	462,191	6.48	3 ^hrs 42 ^mins
10	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,821,384	454,953	6.20	3 ^hrs 52 ^mins
11	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	2,798,045	453,359	6.17	3 ^hrs 53 ^mins
12	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,727,168	440,528	6.19	3 ^hrs 53 ^mins
13	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	2,699,283	447,076	6.04	3 ^hrs 59 ^mins
14	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,461,973	430,121	5.72	4 ^hrs 12 ^mins
15	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,444,061	434,492	5.63	4 ^hrs 16 ^mins
16	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,286,968	382,833	5.97	4 ^hrs 1 ^mins
17	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,272,601	419,559	5.42	4 ^hrs 26 ^mins
18	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,198,552	412,913	5.32	4 ^hrs 30 ^mins
19	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,172,172	413,167	5.26	4 ^hrs 34 ^mins

20	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,108,602	412,147	5.12	4 ^hrs 41 ^mins
21	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,854,643	394,364	4.70	5 ^hrs 6 ^mins
22	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,648,732	377,042	4.37	5 ^hrs 29 ^mins
23	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,595,965	376,434	4.24	5 ^hrs 40 ^mins
24	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,557,443	371,851	4.19	5 ^hrs 44 ^mins
25	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,384,384	359,188	3.85	6 ^hrs 14 ^mins
26	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,256,246	347,829	3.61	6 ^hrs 39 ^mins
27	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,226,602	334,895	3.66	6 ^hrs 33 ^mins
28	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,206,449	340,500	3.54	6 ^hrs 46 ^mins
29	GeForce RTX 2060 Mobile / Max-Q TU106M [GeForce RTX 2060 Mobile / Max-Q] 4550	Nvidia	TU106M	1,190,969	340,474	3.50	6 ^hrs 52 ^mins
30	Radeon RX 5600 OEM/5600 XT/5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT/5700/5700 XT]	AMD	Navi 10	1,177,411	337,932	3.48	6 ^hrs 53 ^mins
31	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,166,288	337,800	3.45	6 ^hrs 57 ^mins
32	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,148,162	334,181	3.44	6 ^hrs 59 ^mins
33	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,128,492	333,299	3.39	7 ^hrs 5 ^mins
34	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,117,251	334,864	3.34	7 ^hrs 12 ^mins
35	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	1,011,201	323,593	3.12	7 ^hrs 41 ^mins
36	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	985,461	318,477	3.09	7 ^hrs 45 ^mins
37	P104-100 GP104 [P104-100]	Nvidia	GP104	933,838	315,249	2.96	8 ^hrs 6 ^mins
38	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	722,436	289,102	2.50	9 ^hrs 36 ^mins
39	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	701,994	282,344	2.49	9 ^hrs 39 ^mins

40	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	666,276	278,736	2.39	10 ^hrs 2 ^mins
41	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	649,245	279,460	2.32	10 ^hrs 20 ^mins
42	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	624,403	275,597	2.27	10 ^hrs 36 ^mins
43	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	602,933	268,040	2.25	10 ^hrs 40 ^mins
44	P106-100 GP106 [P106-100]	Nvidia	GP106	574,883	268,201	2.14	11 ^hrs 12 ^mins
45	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	509,889	257,708	1.98	12 ^hrs 8 ^mins
46	GeForce GTX 1650 SUPER TU116 [GeForce GTX 1650 SUPER]	Nvidia	TU116	469,630	201,995	2.32	10 ^hrs 19 ^mins
47	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	466,555	250,195	1.86	12 ^hrs 52 ^mins
48	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	458,085	249,211	1.84	13 ^hrs 3 ^mins
49	Quadro T2000 Mobile / Max-Q TU117GLM [Quadro T2000 Mobile / Max-Q]	Nvidia	TU117GLM	381,153	229,233	1.66	14 ^hrs 26 ^mins
50	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	377,275	233,078	1.62	14 ^hrs 50 ^mins
51	P106-090 GP106 [P106-090]	Nvidia	GP106	290,022	213,866	1.36	17 ^hrs 42 ^mins
52	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	286,115	212,599	1.35	17 ^hrs 50 ^mins
53	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	224,521	187,152	1.20	20 ^hrs 0 ^mins
54	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	214,244	192,221	1.11	21 ^hrs 32 ^mins
55	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	177,750	181,608	0.98	24 ^hrs 31 ^mins
56	Radeon HD 7790 Bonaire XT [Radeon HD 7790]	AMD	Bonaire XT	141,586	168,553	0.84	28 ^hrs 34 ^mins
57	Radeon RX Vega gfx902 raven [Radeon RX Vega gfx902]	AMD	raven	72,367	134,404	0.54	44 ^hrs 34 ^mins
58	Radeon R7/R6 360 Series Bonaire [Radeon R7/R6 360 Series]	AMD	Bonaire	70,913	122,604	0.58	41 ^hrs 30 ^mins
59	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	55,774	122,604	0.45	52 ^hrs 45 ^mins

60	Ryzen 4900HS mobile Renoir [Ryzen 4900HS mobile]	AMD	Renoir	42,030	122,604	0.34	70 ^hrs 1 ^mins

Research: COVID-19 Folding Project #17320

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17320

GPU PPD Averages

Research: COVID-19 Folding Project #17320

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages