Folding project #17318, COVID-19 research

Research section Research projects and references

Project #17318 overview

Project Summary AI Beta

This project looks at how the SARS-CoV-2 virus binds to human cells. We're studying the proteins involved and how sugar molecules affect their shapes and interactions. This could help us understand how the virus works and develop new drugs to fight it.

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: 142,497
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 / Virology

SARS-CoV-2 is the virus responsible for causing COVID-19. It's a type of coronavirus that primarily affects the respiratory system. The virus spreads through respiratory droplets and can lead to a range of symptoms from mild to severe.

RBD

Receptor binding domain

Protein Domain: Pharmaceutical ResearchBiochemistry / Structural Biology

The receptor binding domain (RBD) is a specific part of the SARS-CoV-2 spike protein. This region binds to the ACE2 receptor on human cells, allowing the virus to attach and enter.

ACE2

Angiotensin-converting enzyme 2

Protein: MedicineBiochemistry / Cell Biology

ACE2 is a protein found on the surface of many human cells, including those in the lungs and heart. It plays a role in regulating blood pressure and is also the receptor used by SARS-CoV-2 to enter cells.

Glycosylation

The addition of sugar molecules to proteins

Cellular Process: BiotechnologyBiochemistry / Molecular Biology

Glycosylation is a common process in which sugar molecules are attached to proteins. This modification can affect protein folding, stability, and function. In the case of SARS-CoV-2, glycosylation of certain proteins may influence its ability to bind to ACE2.

Markov State Models

Mathematical models that describe the transitions between different states of a system

Computational Method: Pharmaceutical ResearchBiophysics / Systems Biology

Markov State Models are computational tools used to simulate and understand complex biological systems. They can be used to predict protein folding pathways, identify metastable states, and explore the dynamics of interactions between molecules.

Metastable States

States that are stable for a relatively long time but can eventually transition to other states

Scientific Concept: Pharmaceutical ResearchBiophysics / Structural Biology

Metastable states are temporary arrangements of molecules or atoms that exist for a certain period before changing to a more stable configuration. These states play a crucial role in biological processes such as protein folding and enzyme catalysis.

Drug Design

The process of designing and developing new drugs

Scientific Process: BiotechnologyPharmaceutical Research / Medicinal Chemistry

Drug design is a complex multidisciplinary field that involves identifying potential drug targets, synthesizing and screening compounds, and optimizing their efficacy and safety. It plays a vital role in the development of new therapies for diseases.

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	6,209,570	227,201	27.33	0 ^hrs 53 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,062,378	212,354	23.84	1 ^hrs 0 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,630,415	207,795	22.28	1 ^hrs 5 ^mins
4	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,384,676	204,006	21.49	1 ^hrs 7 ^mins
5	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	3,945,999	203,365	19.40	1 ^hrs 14 ^mins
6	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	3,864,253	195,563	19.76	1 ^hrs 13 ^mins
7	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,193,462	182,921	17.46	1 ^hrs 22 ^mins
8	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	3,037,856	181,552	16.73	1 ^hrs 26 ^mins
9	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	2,920,586	179,939	16.23	1 ^hrs 29 ^mins
10	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,906,389	177,680	16.36	1 ^hrs 28 ^mins
11	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	2,860,346	176,722	16.19	1 ^hrs 29 ^mins
12	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,712,503	173,824	15.60	1 ^hrs 32 ^mins
13	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,556,103	169,738	15.06	1 ^hrs 36 ^mins
14	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,486,227	168,079	14.79	1 ^hrs 37 ^mins
15	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,410,683	163,290	14.76	1 ^hrs 38 ^mins
16	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,369,147	165,748	14.29	1 ^hrs 41 ^mins
17	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,176,142	158,094	13.76	1 ^hrs 45 ^mins
18	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	1,995,441	156,790	12.73	1 ^hrs 53 ^mins
19	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	1,993,399	156,217	12.76	1 ^hrs 53 ^mins

20	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	1,944,488	148,991	13.05	1 ^hrs 50 ^mins
21	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,680,379	148,640	11.31	2 ^hrs 7 ^mins
22	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,629,264	146,480	11.12	2 ^hrs 9 ^mins
23	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,607,068	142,875	11.25	2 ^hrs 8 ^mins
24	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,408,337	139,875	10.07	2 ^hrs 23 ^mins
25	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,371,724	138,779	9.88	2 ^hrs 26 ^mins
26	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,347,307	137,894	9.77	2 ^hrs 27 ^mins
27	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,266,346	132,471	9.56	2 ^hrs 31 ^mins
28	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,253,529	134,668	9.31	2 ^hrs 35 ^mins
29	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,126,929	127,327	8.85	2 ^hrs 43 ^mins
30	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,096,509	127,723	8.59	2 ^hrs 48 ^mins
31	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,089,992	128,104	8.51	2 ^hrs 49 ^mins
32	Radeon RX 5600 OEM/5600 XT/5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT/5700/5700 XT]	AMD	Navi 10	1,059,662	126,052	8.41	2 ^hrs 51 ^mins
33	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,055,530	123,829	8.52	2 ^hrs 49 ^mins
34	Tesla M40 GM200GL [Tesla M40] 6844	Nvidia	GM200GL	926,780	121,750	7.61	3 ^hrs 9 ^mins
35	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	884,535	120,111	7.36	3 ^hrs 16 ^mins
36	P104-100 GP104 [P104-100]	Nvidia	GP104	705,671	111,402	6.33	3 ^hrs 47 ^mins
37	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	660,200	107,711	6.13	3 ^hrs 55 ^mins
38	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	636,366	106,759	5.96	4 ^hrs 2 ^mins
39	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	626,078	106,804	5.86	4 ^hrs 6 ^mins

40	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	611,781	105,889	5.78	4 ^hrs 9 ^mins
41	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	561,738	102,667	5.47	4 ^hrs 23 ^mins
42	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	561,226	103,121	5.44	4 ^hrs 25 ^mins
43	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	513,163	95,416	5.38	4 ^hrs 28 ^mins
44	P106-100 GP106 [P106-100]	Nvidia	GP106	475,158	97,670	4.86	4 ^hrs 56 ^mins
45	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	460,325	96,460	4.77	5 ^hrs 2 ^mins
46	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	448,596	95,799	4.68	5 ^hrs 8 ^mins
47	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	442,239	91,127	4.85	4 ^hrs 57 ^mins
48	Quadro T2000 Mobile / Max-Q TU117GLM [Quadro T2000 Mobile / Max-Q]	Nvidia	TU117GLM	435,943	94,626	4.61	5 ^hrs 13 ^mins
49	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	425,067	93,691	4.54	5 ^hrs 17 ^mins
50	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	301,333	83,778	3.60	6 ^hrs 40 ^mins
51	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	286,792	82,196	3.49	6 ^hrs 53 ^mins
52	P106-090 GP106 [P106-090]	Nvidia	GP106	281,803	81,960	3.44	6 ^hrs 59 ^mins
53	Radeon R9 200/300 Series Tonga [Radeon R9 200/300 Series]	AMD	Tonga	241,394	77,779	3.10	7 ^hrs 44 ^mins
54	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	212,624	74,529	2.85	8 ^hrs 25 ^mins
55	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	168,165	69,126	2.43	9 ^hrs 52 ^mins
56	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	157,188	58,316	2.70	8 ^hrs 54 ^mins
57	Radeon R7/R6 360 Series Bonaire [Radeon R7/R6 360 Series]	AMD	Bonaire	70,766	47,120	1.50	15 ^hrs 59 ^mins
58	Radeon RX Vega gfx902 raven [Radeon RX Vega gfx902]	AMD	raven	55,859	43,762	1.28	18 ^hrs 48 ^mins
59	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	51,909	46,574	1.11	21 ^hrs 32 ^mins

60	Radeon APU A4-6000 R2 Mullins [Radeon APU A4-6000 R2]	AMD	Mullins	4,922	29,673	0.17	144 ^hrs 41 ^mins

Research: COVID-19 Folding Project #17318

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17318

GPU PPD Averages

Research: COVID-19 Folding Project #17318

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages