Folding project #13434, COVID-19 research

Research section Research projects and references

Project #13434 overview

Project Summary AI Beta

This project uses computer simulations to study how potential drugs might work against the main enzyme of the SARS-CoV-2 virus. The goal is to help researchers quickly identify promising drug candidates for testing. You can even support this open science project by donating!

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

Calculations that estimate the energy changes associated with chemical reactions.

Technical: BiotechnologyDrug Discovery / Computational Chemistry

Alchemical free energy calculations are a type of computer simulation used in drug discovery to predict how well a molecule will bind to a target protein. This information can be used to prioritize compounds for further testing.

compound design

The process of creating new molecules with desired biological activity.

Technical: PharmaceuticalsDrug Discovery / Medicinal Chemistry

Compound design is a crucial step in drug discovery, where chemists use their knowledge of molecular structures and biological targets to create new molecules that can interact with specific proteins or pathways in the body. This involves designing compounds that have the right shape, charge, and functional groups to bind effectively to their target.

SARS-CoV-2

The virus that causes COVID-19.

Scientific: BiotechnologyVirology / Infectious Disease

SARS-CoV-2 is a type of coronavirus that emerged in late 2019 and rapidly spread worldwide, causing the COVID-19 pandemic. This virus primarily infects the respiratory system and can lead to severe illness, pneumonia, and death.

viral protease

An enzyme produced by viruses that cleaves viral proteins to enable replication.

Scientific: BiotechnologyVirology / Infectious Disease

Viral proteases are essential enzymes for the life cycle of many viruses, including SARS-CoV-2. They cleave (cut) specific viral proteins, which allows the virus to assemble new viral particles and spread infection.

X-ray structures

3D representations of molecules obtained using X-ray crystallography.

Scientific: BiotechnologyStructural Biology / Biochemistry

X-ray structures are detailed 3D models of molecules determined by shining X-rays through crystallized samples. These structures reveal the arrangement of atoms within a molecule, providing crucial insights into its function and interactions with other molecules.

Mpro

Main protease of SARS-CoV-2.

Acronym: BiotechnologyVirology / Infectious Disease

Mpro, also known as 3CL protease, is a key enzyme produced by the SARS-CoV-2 virus. It plays a crucial role in viral replication by cleaving viral proteins, which are necessary for assembling new viral particles and spreading infection.

RCSB

Research Collaboratory for Structural Bioinformatics.

Acronym: BiotechnologyStructural Biology / Bioinformatics

The RCSB Protein Data Bank (PDB) is a comprehensive global database of experimentally determined 3D structures of proteins and nucleic acids. It provides researchers with access to a vast collection of structural data, which is essential for understanding the function and interactions of biomolecules.

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	7,196,163	622,276	11.56	2 ^hrs 5 ^mins
2	GeForce RTX 3080 10GB / 20GB GA102 [GeForce RTX 3080 10GB / 20GB]	Nvidia	GA102	5,645,228	571,572	9.88	2 ^hrs 26 ^mins
3	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,877,724	553,592	8.81	2 ^hrs 43 ^mins
4	TITAN RTX TU102 [TITAN RTX] 16310	Nvidia	TU102	4,686,149	548,727	8.54	2 ^hrs 49 ^mins
5	Radeon RX 6800/6800 XT / 6900 XT Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]	AMD	Navi 21	3,971,076	541,848	7.33	3 ^hrs 16 ^mins
6	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	3,682,156	504,182	7.30	3 ^hrs 17 ^mins
7	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	3,666,017	496,140	7.39	3 ^hrs 15 ^mins
8	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,472,117	490,678	7.08	3 ^hrs 24 ^mins
9	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	3,188,280	481,818	6.62	3 ^hrs 38 ^mins
10	Quadro RTX 6000/8000 TU102GL [Quadro RTX 6000/8000]	Nvidia	TU102GL	3,140,740	479,835	6.55	3 ^hrs 40 ^mins
11	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	3,113,806	475,145	6.55	3 ^hrs 40 ^mins
12	GeForce RTX 2080 SUPER Mobile / Max-Q TU104M [GeForce RTX 2080 SUPER Mobile / Max-Q]	Nvidia	TU104M	3,104,944	477,678	6.50	3 ^hrs 42 ^mins
13	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	2,998,902	469,465	6.39	3 ^hrs 45 ^mins
14	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,855,995	463,601	6.16	3 ^hrs 54 ^mins
15	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,787,056	456,645	6.10	3 ^hrs 56 ^mins
16	GeForce RTX 2070 Rev. A TU106 [GeForce RTX 2070 Rev. A] M 7465	Nvidia	TU106	2,669,015	453,966	5.88	4 ^hrs 5 ^mins
17	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,430,439	436,449	5.57	4 ^hrs 19 ^mins
18	GeForce RTX 2070 TU106 [GeForce RTX 2070] M 6497	Nvidia	TU106	2,375,165	431,618	5.50	4 ^hrs 22 ^mins
19	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,212,877	422,399	5.24	4 ^hrs 35 ^mins

20	Radeon VII Vega 20 [Radeon VII] 13,284	AMD	Vega 20	2,083,866	404,657	5.15	4 ^hrs 40 ^mins
21	Quadro RTX 4000 TU104GL [Quadro RTX 4000]	Nvidia	TU104GL	1,863,706	403,345	4.62	5 ^hrs 12 ^mins
22	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	1,718,116	384,899	4.46	5 ^hrs 23 ^mins
23	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,673,725	382,230	4.38	5 ^hrs 29 ^mins
24	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,567,507	378,189	4.14	5 ^hrs 47 ^mins
25	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,520,985	375,078	4.06	5 ^hrs 55 ^mins
26	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,482,321	362,583	4.09	5 ^hrs 52 ^mins
27	GeForce GTX Titan X GM200 [GeForce GTX Titan X] 6144	Nvidia	GM200	1,445,256	370,510	3.90	6 ^hrs 9 ^mins
28	Radeon RX 5600/5600 XT - 5700/5700 XT Navi 10 [Radeon RX 5600 OEM/5600 XT / 5700/5700 XT]	AMD	Navi 10	1,407,840	351,685	4.00	5 ^hrs 60 ^mins
29	GeForce GTX 1070 Ti GP104 [GeForce GTX 1070 Ti] 8186	Nvidia	GP104	1,389,522	349,982	3.97	6 ^hrs 3 ^mins
30	GeForce GTX 1660 Ti TU116 [GeForce GTX 1660 Ti]	Nvidia	TU116	1,287,493	356,229	3.61	6 ^hrs 38 ^mins
31	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,267,509	353,941	3.58	6 ^hrs 42 ^mins
32	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,229,100	347,042	3.54	6 ^hrs 47 ^mins
33	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,039,162	330,024	3.15	7 ^hrs 37 ^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	981,594	318,494	3.08	7 ^hrs 47 ^mins
35	GeForce GTX 1060 3GB GP106 [GeForce GTX 1060 3GB] 3935	Nvidia	GP106	943,633	318,314	2.96	8 ^hrs 6 ^mins
36	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	934,692	315,074	2.97	8 ^hrs 5 ^mins
37	GeForce GTX 1650 Ti Mobile TU116M [GeForce GTX 1650 Ti Mobile]	Nvidia	TU116M	874,539	311,313	2.81	8 ^hrs 33 ^mins
38	GeForce GTX 1070 GP104 [GeForce GTX 1070]	Nvidia	GP104	786,640	302,176	2.60	9 ^hrs 13 ^mins
39	P104-100 GP104 [P104-100]	Nvidia	GP104	718,449	290,417	2.47	9 ^hrs 42 ^mins

40	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	715,624	292,925	2.44	9 ^hrs 49 ^mins
41	GeForce GTX 1650 TU116 [GeForce GTX 1650] 2984	Nvidia	TU116	574,519	272,684	2.11	11 ^hrs 23 ^mins
42	Radeon R9 Fury X Fiji XT [Radeon R9 Fury X]	AMD	Fiji XT	547,224	219,143	2.50	9 ^hrs 37 ^mins
43	Radeon R9 200/300X Series Hawaii [Radeon R9 200/300X Series]	AMD	Hawaii	487,787	257,857	1.89	12 ^hrs 41 ^mins
44	Radeon RX 470/480/570/580/590 Ellesmere XT [Radeon RX 470/480/570/580/590]	AMD	Ellesmere XT	484,475	256,745	1.89	12 ^hrs 43 ^mins
45	Radeon R9 200/300 Series Hawaii [Radeon R9 200/300 Series]	AMD	Hawaii	461,085	241,072	1.91	12 ^hrs 33 ^mins
46	Quadro T2000 Mobile / Max-Q TU117GLM [Quadro T2000 Mobile / Max-Q]	Nvidia	TU117GLM	413,272	201,071	2.06	11 ^hrs 41 ^mins
47	P106-100 GP106 [P106-100]	Nvidia	GP106	397,636	241,039	1.65	14 ^hrs 33 ^mins
48	P106-090 GP106 [P106-090]	Nvidia	GP106	289,122	217,239	1.33	18 ^hrs 2 ^mins
49	Radeon R9 280/HD 7900/8950 Tahiti PRO [Radeon R9 280/HD 7900/8950]	AMD	Tahiti PRO	288,836	216,449	1.33	17 ^hrs 59 ^mins
50	Quadro P1000 GP107GL [Quadro P1000]	Nvidia	GP107GL	274,259	212,896	1.29	18 ^hrs 38 ^mins
51	Quadro T1000 Mobile TU117GLM [Quadro T1000 Mobile]	Nvidia	TU117GLM	257,694	200,262	1.29	18 ^hrs 39 ^mins
52	GeForce GTX 1050 Ti GP107 [GeForce GTX 1050 Ti] 2138	Nvidia	GP107	236,598	194,272	1.22	19 ^hrs 42 ^mins
53	Radeon HD 7800 Pitcairn [Radeon HD 7800]	AMD	Pitcairn	185,325	186,849	0.99	24 ^hrs 12 ^mins
54	Radeon RX Vega M XL [Radeon RX Vega M XL]	AMD	Vega	175,795	165,630	1.06	22 ^hrs 37 ^mins
55	Radeon R7 250/HD 7700 R575A [Radeon R7 250/HD 7700]	AMD	R575A	48,715	125,550	0.39	61 ^hrs 51 ^mins
56	Ryzen 4900HS mobile Renoir [Ryzen 4900HS mobile]	AMD	Renoir	33,148	125,550	0.26	90 ^hrs 54 ^mins

Research: COVID-19 Folding Project #13434

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 13434

GPU PPD Averages

Research: COVID-19 Folding Project #13434

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages