Folding project #17315, COVID-19 research

Research section Research projects and references

Project #17315 overview

Project Summary AI Beta

This project studies how the SARS-CoV-2 virus attaches to human cells. Scientists are using computer simulations to see how proteins on the virus (RBD) and in our bodies (ACE2) interact. They're also looking at how sugar molecules affect these interactions. This research could help scientists design 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: 202,867
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, HealthcareDisease / Infectious Disease

SARS-CoV-2 is a virus that causes the disease COVID-19. It is a type of coronavirus, which are common viruses that can cause mild to severe respiratory illnesses.

RBD

Receptor binding domain

Protein: Pharmaceuticals, BiotechnologyBiotechnology / Structural Biology

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. It binds to the ACE2 receptor on the surface of cells.

ACE2

Angiotensin-converting enzyme 2

Protein: Pharmaceuticals, BiotechnologyBiotechnology / 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 a receptor to enter cells.

Glycosylation

The addition of sugar molecules to proteins.

Biochemical Process: Pharmaceuticals, BiotechnologyBiotechnology / Cellular Biology

Glycosylation is a process where 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.

Computational Method: Pharmaceuticals, BiotechnologyBiotechnology / Systems Biology

Markov state models are a powerful tool for understanding how complex systems change over time. They can be used to study biological processes, such as protein folding and drug binding.

Metastable States

Temporary stable states that are not the lowest energy state of a system.

Scientific Concept: Pharmaceuticals, BiotechnologyBiotechnology / Structural Biology

Metastable states are like temporary resting points in a complex system. They are relatively stable but can easily transition to other states.

Drug Design

The process of designing and developing new drugs.

Process: Pharmaceuticals, BiotechnologyPharmaceuticals / Medicinal Chemistry

Drug design is a complex process that involves identifying potential drug targets, designing molecules that interact with these targets, and testing the effectiveness and safety of the resulting drugs.

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	6,639,981	341,888	19.42	1 ^hrs 14 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,362,760	318,404	16.84	1 ^hrs 25 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	5,074,777	314,725	16.12	1 ^hrs 29 ^mins
4	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,537,683	302,765	14.99	1 ^hrs 36 ^mins
5	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	4,146,441	293,576	14.12	1 ^hrs 42 ^mins
6	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	4,031,378	286,820	14.06	1 ^hrs 42 ^mins
7	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,856,516	285,504	13.51	1 ^hrs 47 ^mins
8	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,330,046	272,941	12.20	1 ^hrs 58 ^mins
9	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,997,927	262,111	11.44	2 ^hrs 6 ^mins
10	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,888,504	260,417	11.09	2 ^hrs 10 ^mins
11	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,870,846	258,140	11.12	2 ^hrs 9 ^mins
12	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	2,830,031	258,687	10.94	2 ^hrs 12 ^mins
13	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,737,848	256,240	10.68	2 ^hrs 15 ^mins
14	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER]	Nvidia	TU104	2,714,075	256,003	10.60	2 ^hrs 16 ^mins
15	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,572,704	250,698	10.26	2 ^hrs 20 ^mins
16	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,568,135	249,552	10.29	2 ^hrs 20 ^mins
17	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,337,294	241,329	9.69	2 ^hrs 29 ^mins
18	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,327,354	240,135	9.69	2 ^hrs 29 ^mins
19	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	2,253,387	239,369	9.41	2 ^hrs 33 ^mins

20	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,147,548	234,078	9.17	2 ^hrs 37 ^mins
21	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,100,340	230,321	9.12	2 ^hrs 38 ^mins
22	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,775,040	219,341	8.09	2 ^hrs 58 ^mins
23	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,654,094	216,203	7.65	3 ^hrs 8 ^mins
24	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,635,893	214,403	7.63	3 ^hrs 9 ^mins
25	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,356,736	200,584	6.76	3 ^hrs 33 ^mins
26	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,342,392	194,868	6.89	3 ^hrs 29 ^mins
27	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,300,459	200,040	6.50	3 ^hrs 42 ^mins
28	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,299,894	200,208	6.49	3 ^hrs 42 ^mins
29	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,201,953	191,653	6.27	3 ^hrs 50 ^mins
30	GeForce RTX 2060 Mobile / Max-Q TU106M [GeForce RTX 2060 Mobile / Max-Q] 4550	Nvidia	TU106M	1,181,357	193,234	6.11	3 ^hrs 56 ^mins
31	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,141,594	190,273	6.00	4 ^hrs 0 ^mins
32	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,138,799	191,079	5.96	4 ^hrs 2 ^mins
33	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,130,594	190,766	5.93	4 ^hrs 3 ^mins
34	Radeon RX 5600 OEM/5600 XT/5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT/5700/5700 XT]	AMD	Navi 10	975,280	175,973	5.54	4 ^hrs 20 ^mins
35	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	970,345	180,176	5.39	4 ^hrs 27 ^mins
36	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	914,454	174,984	5.23	4 ^hrs 36 ^mins
37	P104-100 GP104 [P104-100]	Nvidia	GP104	866,560	174,760	4.96	4 ^hrs 50 ^mins
38	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	688,709	157,513	4.37	5 ^hrs 29 ^mins
39	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	646,794	158,566	4.08	5 ^hrs 53 ^mins

40	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	603,025	154,424	3.90	6 ^hrs 9 ^mins
41	GeForce GTX 1650 SUPER TU116 [GeForce GTX 1650 SUPER]	Nvidia	TU116	590,457	136,477	4.33	5 ^hrs 33 ^mins
42	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	568,931	152,012	3.74	6 ^hrs 25 ^mins
43	P106-100 GP106 [P106-100]	Nvidia	GP106	561,227	151,271	3.71	6 ^hrs 28 ^mins
44	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	558,754	148,842	3.75	6 ^hrs 24 ^mins
45	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	509,843	144,069	3.54	6 ^hrs 47 ^mins
46	Quadro T2000 Mobile / Max-Q TU117GLM [Quadro T2000 Mobile / Max-Q]	Nvidia	TU117GLM	489,527	145,014	3.38	7 ^hrs 7 ^mins
47	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	487,949	142,602	3.42	7 ^hrs 1 ^mins
48	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	484,603	144,406	3.36	7 ^hrs 9 ^mins
49	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	470,093	142,617	3.30	7 ^hrs 17 ^mins
50	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	453,119	140,573	3.22	7 ^hrs 27 ^mins
51	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	391,509	133,342	2.94	8 ^hrs 10 ^mins
52	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	320,351	125,586	2.55	9 ^hrs 25 ^mins
53	P106-090 GP106 [P106-090]	Nvidia	GP106	295,561	122,264	2.42	9 ^hrs 56 ^mins
54	Radeon R9 200/300 Series Tonga [Radeon R9 200/300 Series]	AMD	Tonga	255,821	116,442	2.20	10 ^hrs 55 ^mins
55	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	212,767	109,260	1.95	12 ^hrs 19 ^mins
56	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	193,436	100,386	1.93	12 ^hrs 27 ^mins
57	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	166,407	101,026	1.65	14 ^hrs 34 ^mins
58	Radeon R7/R6 360 Series Bonaire [Radeon R7/R6 360 Series]	AMD	Bonaire	81,667	80,060	1.02	23 ^hrs 32 ^mins
59	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	52,012	68,490	0.76	31 ^hrs 36 ^mins

60	Radeon R7 250/HD 7700 R575A [Radeon R7 250/HD 7700]	AMD	R575A	42,667	63,706	0.67	35 ^hrs 50 ^mins

Research: COVID-19 Folding Project #17315

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17315

GPU PPD Averages

Research: COVID-19 Folding Project #17315

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages