Folding project #17322, COVID-19 research

Research section Research projects and references

Project #17322 overview

Project Summary AI Beta

This project studies how sugar molecules (glycosylation) affect the shape and behavior of proteins involved in COVID-19 infection. By simulating these proteins, scientists aim to understand how glycosylation influences their interaction and identify potential drug targets.

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: 434,648
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: Biotechnology, PharmaceuticalsInfectious Disease / Virology

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.

Receptor Binding Domain (RBD)

The part of a virus protein that binds to a host cell receptor

Protein: Biotechnology, PharmaceuticalsBiochemistry / Structural Biology

The RBD is a region on the surface of some viral proteins that allows them to attach to specific receptors on host cells. This binding is essential for the virus to enter and infect the cell.

ACE2

Angiotensin-converting enzyme 2

Protein: Biotechnology, PharmaceuticalsBiochemistry / Cellular Biology

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

Glycosylation

The process of adding sugar molecules to proteins

Bioprocess: Biotechnology, PharmaceuticalsBiochemistry / Molecular Biology

Glycosylation is a common modification of proteins that can affect their structure, function, and stability. It plays a role in many biological processes, including immune response, cell signaling, and protein folding.

Markov State Models

Mathematical models used to describe the dynamics of complex systems

Computational Model: Biotechnology, PharmaceuticalsBiophysics / Structural Biology

Markov State Models are a type of computational tool used to simulate and analyze the behavior of complex systems over time. They are often applied in biophysics to study protein folding, molecular interactions, and cellular processes.

Metastable States

Temporary, stable states of a system that are not its lowest energy state

Scientific Concept: Biotechnology, PharmaceuticalsBiophysics / Structural Biology

Metastable states are like temporary resting points for complex systems. They represent configurations that are relatively stable but not the most stable. Understanding these states can help us understand how systems transition between different configurations and how they respond to changes.

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	6,691,388	354,404	18.88	1 ^hrs 16 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,222,056	323,916	16.12	1 ^hrs 29 ^mins
3	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	4,681,637	318,804	14.69	1 ^hrs 38 ^mins
4	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,495,887	315,470	14.25	1 ^hrs 41 ^mins
5	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,203,768	307,411	13.67	1 ^hrs 45 ^mins
6	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	4,043,093	303,199	13.33	1 ^hrs 48 ^mins
7	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,527,420	290,890	12.13	1 ^hrs 59 ^mins
8	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,274,759	282,661	11.59	2 ^hrs 4 ^mins
9	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,882,148	269,946	10.68	2 ^hrs 15 ^mins
10	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,782,321	268,488	10.36	2 ^hrs 19 ^mins
11	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,704,454	265,111	10.20	2 ^hrs 21 ^mins
12	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,582,038	260,697	9.90	2 ^hrs 25 ^mins
13	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	2,579,865	259,819	9.93	2 ^hrs 25 ^mins
14	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	2,551,513	260,588	9.79	2 ^hrs 27 ^mins
15	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,431,558	255,473	9.52	2 ^hrs 31 ^mins
16	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,358,401	253,336	9.31	2 ^hrs 35 ^mins
17	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,232,917	242,790	9.20	2 ^hrs 37 ^mins
18	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,187,794	247,224	8.85	2 ^hrs 43 ^mins
19	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,157,292	245,123	8.80	2 ^hrs 44 ^mins

20	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,014,520	237,714	8.47	2 ^hrs 50 ^mins
21	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,803,752	231,998	7.77	3 ^hrs 5 ^mins
22	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,764,330	230,702	7.65	3 ^hrs 8 ^mins
23	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,577,993	218,606	7.22	3 ^hrs 19 ^mins
24	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,554,392	220,853	7.04	3 ^hrs 25 ^mins
25	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,343,715	210,528	6.38	3 ^hrs 46 ^mins
26	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,266,793	206,152	6.14	3 ^hrs 54 ^mins
27	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,258,650	202,428	6.22	3 ^hrs 52 ^mins
28	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,193,113	201,705	5.92	4 ^hrs 3 ^mins
29	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,159,533	200,526	5.78	4 ^hrs 9 ^mins
30	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,146,398	198,454	5.78	4 ^hrs 9 ^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	1,131,196	194,972	5.80	4 ^hrs 8 ^mins
32	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,102,232	196,477	5.61	4 ^hrs 17 ^mins
33	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,083,244	195,719	5.53	4 ^hrs 20 ^mins
34	P104-100 GP104 [P104-100]	Nvidia	GP104	910,554	185,185	4.92	4 ^hrs 53 ^mins
35	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	835,928	177,996	4.70	5 ^hrs 7 ^mins
36	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	779,454	156,292	4.99	4 ^hrs 49 ^mins
37	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	630,744	163,711	3.85	6 ^hrs 14 ^mins
38	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	629,514	160,805	3.91	6 ^hrs 8 ^mins
39	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	613,827	160,671	3.82	6 ^hrs 17 ^mins

40	P106-100 GP106 [P106-100]	Nvidia	GP106	564,627	157,979	3.57	6 ^hrs 43 ^mins
41	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	561,462	145,224	3.87	6 ^hrs 12 ^mins
42	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	487,571	138,963	3.51	6 ^hrs 50 ^mins
43	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	468,537	148,385	3.16	7 ^hrs 36 ^mins
44	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	468,433	147,748	3.17	7 ^hrs 34 ^mins
45	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	451,376	145,805	3.10	7 ^hrs 45 ^mins
46	GeForce GTX 1650 SUPER TU116 [GeForce GTX 1650 SUPER]	Nvidia	TU116	389,536	108,538	3.59	6 ^hrs 41 ^mins
47	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	368,637	136,961	2.69	8 ^hrs 55 ^mins
48	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	308,826	129,247	2.39	10 ^hrs 3 ^mins
49	P106-090 GP106 [P106-090]	Nvidia	GP106	281,744	125,161	2.25	10 ^hrs 40 ^mins
50	Radeon R9 200/300 Series Tonga [Radeon R9 200/300 Series]	AMD	Tonga	273,510	123,650	2.21	10 ^hrs 51 ^mins
51	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	213,213	114,370	1.86	12 ^hrs 52 ^mins
52	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	198,516	92,252	2.15	11 ^hrs 9 ^mins
53	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	173,524	106,576	1.63	14 ^hrs 44 ^mins
54	Radeon R9 200 Series Hawaii [Radeon R9 200 Series]	AMD	Hawaii	156,463	101,773	1.54	15 ^hrs 37 ^mins
55	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	152,966	77,806	1.97	12 ^hrs 12 ^mins
56	Radeon RX Vega gfx902 raven [Radeon RX Vega gfx902]	AMD	raven	69,552	78,449	0.89	27 ^hrs 4 ^mins
57	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	63,693	73,507	0.87	27 ^hrs 42 ^mins
58	Ryzen 4900HS mobile Renoir [Ryzen 4900HS mobile]	AMD	Renoir	53,210	72,421	0.73	32 ^hrs 40 ^mins
59	Radeon R7 250/HD 7700 R575A [Radeon R7 250/HD 7700]	AMD	R575A	45,305	63,463	0.71	33 ^hrs 37 ^mins

Research: COVID-19 Folding Project #17322

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17322

GPU PPD Averages

Research: COVID-19 Folding Project #17322

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages