Folding project #13437, COVID-19 research

Research section Research projects and references

Project #13437 overview

Project Summary AI Beta

This project uses computer simulations to study a key protein from the COVID-19 virus. By analyzing how different molecules interact with this protein, researchers can identify potential drugs that could help treat the disease. The project is part of a larger effort called the COVID Moonshot, which aims to rapidly develop new and affordable treatments for COVID-19.

Automated summary; simplified and may not be fully accurate.

Project team

Manager(s): Prof. John Chodera
Institution: Memorial Sloan Kettering Cancer Center
Website: Open project site

Work unit

Atoms: 89,709
Core: OPENMM_22
Status: Beta

Source material

Official Project Description

https://www.youtube.com/watch?v=VnyaAmM1nhE These projects are to assist rapid sprints of relative alchemical free energy calculations for prioritizing compound designs from chemists from the COVID Moonshot for synthesis. This series of projects simulates the SARS-CoV-2 main viral protease. These projects collectively cover the entire set of X-ray structures collected by the COVID Moonshot, and more RUNs will be added as new structures are collected. To learn more about what the Moonshot is and how it came about, you can read our blog post or watch this video. In addition to helping us prioritize compounds, you can help us purchase more compounds for synthesis at cost from Enamine by sponsoring our GoFundMe page for patent-free open science COVID-19 drug discovery! This is a radical new approach to drug discovery that aims to rapidly produce inexpensive new therapies. SARS-CoV-2 main viral potease (Mpro) with ligand bound, from the RCSB.

Reading reference

Related Terms Glossary AI Beta

Automated high-level definitions; simplified and may not be fully accurate.

alchemical free energy calculations

Calculating the energy changes in molecules during chemical reactions.

Technical: BiotechnologyDrug Discovery / Computational Chemistry

Alchemical free energy calculations are a computational method used to predict how molecules will interact with each other. This helps scientists design new drugs and understand how existing drugs work.

compound designs

The creation of new chemical compounds with specific properties.

Technical: PharmaceuticalsDrug Discovery / Medicinal Chemistry

Compound designs involve the development of novel molecules with desired biological activities, often for therapeutic purposes.

SARS-CoV-2

The virus responsible for COVID-19.

Scientific: BiotechnologyVirology / Infectious Diseases

SARS-CoV-2 is a coronavirus that causes the disease COVID-19. It has spread globally, leading to significant public health concerns.

viral protease

An enzyme essential for viral replication.

Scientific: BiotechnologyVirology / Infectious Diseases

Viral proteases are enzymes that viruses need to replicate. They cut proteins into smaller pieces, allowing the virus to build new copies of itself.

X-ray structures

Three-dimensional representations of molecules obtained using X-ray crystallography.

Scientific: BiotechnologyStructural Biology / Biochemistry

X-ray structures provide detailed information about the shape and arrangement of atoms within molecules. This is crucial for understanding how proteins and other biomolecules function.

RCSB

Protein Data Bank.

Acronym: BiotechnologyStructural Biology / Bioinformatics

The RCSB (Research Collaboratory for Structural Bioinformatics) is a database that provides access to 3D structural information about biological macromolecules.

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	7,140,621	622,657	11.47	2 ^hrs 6 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,412,193	558,297	9.69	2 ^hrs 29 ^mins
3	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	5,350,352	565,415	9.46	2 ^hrs 32 ^mins
4	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,764,808	549,913	8.66	2 ^hrs 46 ^mins
5	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	3,855,110	504,017	7.65	3 ^hrs 8 ^mins
6	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	3,830,147	509,007	7.52	3 ^hrs 11 ^mins
7	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,515,028	493,139	7.13	3 ^hrs 22 ^mins
8	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	3,319,436	488,076	6.80	3 ^hrs 32 ^mins
9	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	3,176,839	479,347	6.63	3 ^hrs 37 ^mins
10	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,050,192	478,604	6.37	3 ^hrs 46 ^mins
11	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,936,646	460,897	6.37	3 ^hrs 46 ^mins
12	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,807,245	456,434	6.15	3 ^hrs 54 ^mins
13	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	2,806,021	389,151	7.21	3 ^hrs 20 ^mins
14	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,777,332	458,310	6.06	3 ^hrs 58 ^mins
15	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,690,679	451,052	5.97	4 ^hrs 1 ^mins
16	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,517,285	442,501	5.69	4 ^hrs 13 ^mins
17	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	2,426,019	437,221	5.55	4 ^hrs 20 ^mins
18	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,300,726	430,268	5.35	4 ^hrs 29 ^mins
19	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,179,979	410,465	5.31	4 ^hrs 31 ^mins

20	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	1,915,590	405,926	4.72	5 ^hrs 5 ^mins
21	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,901,470	401,826	4.73	5 ^hrs 4 ^mins
22	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,641,793	377,472	4.35	5 ^hrs 31 ^mins
23	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,540,675	376,370	4.09	5 ^hrs 52 ^mins
24	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,496,103	374,647	3.99	6 ^hrs 1 ^mins
25	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,483,266	367,371	4.04	5 ^hrs 57 ^mins
26	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,481,129	374,384	3.96	6 ^hrs 4 ^mins
27	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,357,954	360,514	3.77	6 ^hrs 22 ^mins
28	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,352,454	355,139	3.81	6 ^hrs 18 ^mins
29	Radeon RX 5600/5600 XT - 5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT / 5700/5700 XT]	AMD	Navi 10	1,341,206	341,831	3.92	6 ^hrs 7 ^mins
30	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,295,320	355,952	3.64	6 ^hrs 36 ^mins
31	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,154,259	337,114	3.42	7 ^hrs 1 ^mins
32	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,100,414	335,548	3.28	7 ^hrs 19 ^mins
33	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	1,084,911	336,650	3.22	7 ^hrs 27 ^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	1,033,007	327,554	3.15	7 ^hrs 37 ^mins
35	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	853,779	308,235	2.77	8 ^hrs 40 ^mins
36	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	738,140	296,022	2.49	9 ^hrs 37 ^mins
37	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	726,441	294,179	2.47	9 ^hrs 43 ^mins
38	P104-100 GP104 [P104-100]	Nvidia	GP104	581,325	273,926	2.12	11 ^hrs 19 ^mins
39	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	532,101	257,544	2.07	11 ^hrs 37 ^mins

40	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	527,963	265,224	1.99	12 ^hrs 3 ^mins
41	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	510,135	261,585	1.95	12 ^hrs 18 ^mins
42	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	446,270	244,203	1.83	13 ^hrs 8 ^mins
43	P106-100 GP106 [P106-100]	Nvidia	GP106	423,593	246,142	1.72	13 ^hrs 57 ^mins
44	P106-090 GP106 [P106-090]	Nvidia	GP106	342,250	229,232	1.49	16 ^hrs 4 ^mins
45	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	323,218	224,966	1.44	16 ^hrs 42 ^mins
46	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	279,955	198,797	1.41	17 ^hrs 3 ^mins
47	GeForce GTX 1050 Ti GP107 [GeForce GTX 1050 Ti] 2138	Nvidia	GP107	251,968	198,410	1.27	18 ^hrs 54 ^mins
48	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	221,326	198,247	1.12	21 ^hrs 30 ^mins
49	Radeon RX 5500/5500M / Pro 5500M Navi 14 [Radeon RX 5500/5500M / Pro 5500M]	AMD	Navi 14	206,882	141,580	1.46	16 ^hrs 25 ^mins
50	Radeon R9 200/300 Series Tonga [Radeon R9 200/300 Series]	AMD	Tonga	195,325	191,881	1.02	23 ^hrs 35 ^mins
51	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	147,002	173,187	0.85	28 ^hrs 17 ^mins
52	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	145,268	145,542	1.00	24 ^hrs 3 ^mins
53	Radeon HD 7790 Bonaire XT [Radeon HD 7790]	AMD	Bonaire XT	115,999	159,700	0.73	33 ^hrs 2 ^mins
54	Radeon R7 250/HD 7700 R575A [Radeon R7 250/HD 7700]	AMD	R575A	53,612	125,550	0.43	56 ^hrs 12 ^mins

Research: COVID-19 Folding Project #13437

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 13437

GPU PPD Averages

Research: COVID-19 Folding Project #13437

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages