Folding project #17317, COVID-19 research

Research section Research projects and references

Project #17317 overview

Project Summary AI Beta

The project relates to understanding how the virus protein (RBD) attaches to human cells using simulations. Researchers will study RBD alone and with a human receptor (ACE2), with and without added sugars. This helps understand how sugars affect the virus's shape and how it binds to cells. The goal is to use this knowledge to design better drugs.

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: 143,492
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 that causes COVID-19. It's a type of coronavirus, which are common in animals but can sometimes infect humans. This particular virus emerged in late 2019 and spread rapidly worldwide.

Receptor Binding Domain (RBD)

Receptor binding domain

Protein: PharmacologyBiochemistry / 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 enter and infect them.

ACE2

Angiotensin-converting enzyme 2

Protein: MedicineBiochemistry / 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 its entry point into human cells.

Glycosylation

The addition of sugar molecules to proteins or lipids

Biochemical Process: BiotechnologyBiochemistry / Molecular Biology

Glycosylation is a common process where sugar molecules are attached to proteins. This can affect the protein's shape, function, and stability. In the case of viruses like SARS-CoV-2, glycosylation can influence how they interact with human cells.

Markov State Model

A statistical model used to describe the dynamics of a system over time

Computational Tool: PharmacologyBioinformatics / Molecular Dynamics

Markov State Models are used in computational biology to simulate how molecules move and interact. They can help researchers understand complex biological processes like protein folding and virus binding.

Metastable States

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

Physical Property: PharmacologyChemistry / Physical Chemistry

Metastable states are like temporary resting points in a system. They might seem stable for a while, but eventually, the system will move on to a different state. Understanding metastable states is important in fields like drug design because it can help explain how molecules interact and behave.

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	6,178,396	234,886	26.30	0 ^hrs 55 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,257,567	223,471	23.53	1 ^hrs 1 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,537,681	214,750	21.13	1 ^hrs 8 ^mins
4	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,237,903	209,632	20.22	1 ^hrs 11 ^mins
5	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	4,115,678	207,749	19.81	1 ^hrs 13 ^mins
6	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	3,885,578	203,653	19.08	1 ^hrs 15 ^mins
7	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,212,979	192,258	16.71	1 ^hrs 26 ^mins
8	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,160,842	190,101	16.63	1 ^hrs 27 ^mins
9	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,929,552	186,528	15.71	1 ^hrs 32 ^mins
10	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,872,787	183,519	15.65	1 ^hrs 32 ^mins
11	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	2,764,979	181,240	15.26	1 ^hrs 34 ^mins
12	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,655,728	178,859	14.85	1 ^hrs 37 ^mins
13	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	2,537,101	179,229	14.16	1 ^hrs 42 ^mins
14	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,510,714	175,781	14.28	1 ^hrs 41 ^mins
15	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,479,486	173,939	14.25	1 ^hrs 41 ^mins
16	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,304,492	171,228	13.46	1 ^hrs 47 ^mins
17	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,294,763	166,416	13.79	1 ^hrs 44 ^mins
18	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,268,580	169,343	13.40	1 ^hrs 47 ^mins
19	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,004,864	161,104	12.44	1 ^hrs 56 ^mins

20	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	1,945,475	160,561	12.12	1 ^hrs 59 ^mins
21	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,604,298	151,942	10.56	2 ^hrs 16 ^mins
22	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,576,014	150,477	10.47	2 ^hrs 17 ^mins
23	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,492,599	142,870	10.45	2 ^hrs 18 ^mins
24	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,372,008	143,886	9.54	2 ^hrs 31 ^mins
25	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,353,929	142,854	9.48	2 ^hrs 32 ^mins
26	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,300,813	141,598	9.19	2 ^hrs 37 ^mins
27	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,292,431	141,318	9.15	2 ^hrs 37 ^mins
28	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,211,108	137,583	8.80	2 ^hrs 44 ^mins
29	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,139,364	134,593	8.47	2 ^hrs 50 ^mins
30	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,096,294	133,539	8.21	2 ^hrs 55 ^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	1,093,110	130,867	8.35	2 ^hrs 52 ^mins
32	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,054,187	131,471	8.02	2 ^hrs 60 ^mins
33	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,036,196	126,689	8.18	2 ^hrs 56 ^mins
34	Tesla M40 GM200GL [Tesla M40] 6844	Nvidia	GM200GL	1,013,243	130,302	7.78	3 ^hrs 5 ^mins
35	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	670,795	98,249	6.83	3 ^hrs 31 ^mins
36	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	663,339	113,608	5.84	4 ^hrs 7 ^mins
37	P104-100 GP104 [P104-100]	Nvidia	GP104	641,086	112,142	5.72	4 ^hrs 12 ^mins
38	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	636,165	110,445	5.76	4 ^hrs 10 ^mins
39	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	632,826	110,506	5.73	4 ^hrs 11 ^mins

40	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	630,709	111,382	5.66	4 ^hrs 14 ^mins
41	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	627,659	110,907	5.66	4 ^hrs 14 ^mins
42	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	587,705	107,439	5.47	4 ^hrs 23 ^mins
43	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	543,292	105,891	5.13	4 ^hrs 41 ^mins
44	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	541,937	102,718	5.28	4 ^hrs 33 ^mins
45	GeForce GTX 1650 SUPER TU116 [GeForce GTX 1650 SUPER]	Nvidia	TU116	508,636	94,388	5.39	4 ^hrs 27 ^mins
46	Quadro T2000 Mobile / Max-Q TU117GLM [Quadro T2000 Mobile / Max-Q]	Nvidia	TU117GLM	458,831	100,328	4.57	5 ^hrs 15 ^mins
47	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	452,793	99,641	4.54	5 ^hrs 17 ^mins
48	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	448,892	99,713	4.50	5 ^hrs 20 ^mins
49	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	435,546	94,518	4.61	5 ^hrs 12 ^mins
50	P106-100 GP106 [P106-100]	Nvidia	GP106	434,328	98,397	4.41	5 ^hrs 26 ^mins
51	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	324,096	89,349	3.63	6 ^hrs 37 ^mins
52	P106-090 GP106 [P106-090]	Nvidia	GP106	273,229	84,271	3.24	7 ^hrs 24 ^mins
53	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	268,561	83,641	3.21	7 ^hrs 28 ^mins
54	Radeon R9 200/300 Series Tonga [Radeon R9 200/300 Series]	AMD	Tonga	232,686	79,080	2.94	8 ^hrs 9 ^mins
55	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	195,115	75,613	2.58	9 ^hrs 18 ^mins
56	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	176,583	72,717	2.43	9 ^hrs 53 ^mins
57	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	154,372	56,477	2.73	8 ^hrs 47 ^mins
58	Radeon R7/R6 360 Series Bonaire [Radeon R7/R6 360 Series]	AMD	Bonaire	76,675	55,524	1.38	17 ^hrs 23 ^mins
59	Ryzen vega 8 mobile Raven [Ryzen vega 8 mobile]	AMD	Raven	53,271	48,736	1.09	21 ^hrs 57 ^mins

Research: COVID-19 Folding Project #17317

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 17317

GPU PPD Averages

Research: COVID-19 Folding Project #17317

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages