Folding project #12117, PROTEIN-BRUSH-POLYMER-SIMULATION research

Research section Research projects and references

Project #12117 overview

Project Summary AI Beta

This project looks at how short proteins (peptides) work better when linked together into chains called "protein brush polymers". These polymers help peptides get inside cells more easily. The project focuses on a specific protein called Trpzip2, which has a folded shape like a beta-sheet. By simulating different arrangements of these protein chains, researchers hope to understand how the shape of the protein affects how well the polymer works.

Automated summary; simplified and may not be fully accurate.

Project team

Manager(s): Hassan Nadeem
Institution: University of Illinois at Urbana-Champaign

Work unit

Atoms: 151,546
Core: 0x22
Status: Public

Source material

Official Project Description

Protein Brush Polymers Short peptides are considered ideal therapeutics because of their small size and bioactivity, however they are prone to enzyme degradation.

Protein Brush Polymers allow peptides to bind to a hydrophobic backbone in a polymeric scheme which enhances the penetration of these peptides in cell/targets. In this project we simulate Trpzip2, which is a beta-hairpin peptide, for investigation of beta-sheet secondary structure effect on the polymer conformation. We have two broad aims in this study.

To simulate the peptide monomer as well as simulate a 15-mer polymer system with different configurations to investigate beta-sheet content.

Reading reference

Related Terms Glossary AI Beta

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

Protein

Large biomolecules essential for structure, function, and regulation of the body.

Scientific: MedicineBiotechnology / Pharmacology

Proteins are complex molecules found in all living things. They perform many vital functions, such as building tissues, transporting substances, and catalyzing chemical reactions.

Brush Polymers

Polymeric materials with side chains projecting outwards like a brush.

Technical: MedicineBiotechnology / Materials Science

Brush polymers are a type of polymer where long chain molecules (the backbone) have smaller chains branching off like bristles. This unique structure gives them special properties that make them useful in various applications.

Peptides

Short chains of amino acids linked together.

Scientific: MedicineBiotechnology / Pharmacology

Peptides are small chains of amino acids, the building blocks of proteins. They play important roles in many biological processes and have potential as therapeutic agents.

Beta-Hairpin

A common secondary structure in proteins characterized by a hairpin-like shape.

Scientific: MedicineBiotechnology / Structural Biology

Beta-hairpins are a type of protein folding pattern where two strands of amino acids are connected by a short loop. This structure is important for many biological functions.

Polymer

A large molecule made up of repeating units called monomers.

Technical: MedicineChemistry / Materials Science

Polymers are long chains of molecules linked together. They have a wide range of properties and are used in many different applications, including plastics, fibers, and adhesives.

Trpzip2

A beta-hairpin peptide used as a model system for studying protein folding.

Scientific: MedicineBiotechnology / Structural Biology

Trpzip2 is a small protein fragment that folds into a specific shape. It is often used by scientists to study how proteins fold and interact with each other.

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 4090 AD102 [GeForce RTX 4090]	Nvidia	AD102	21,770,671	403,849	53.91	0 ^hrs 27 ^mins
2	GeForce RTX 4080 AD103 [GeForce RTX 4080]	Nvidia	AD103	14,990,367	386,193	38.82	0 ^hrs 37 ^mins
3	GeForce RTX 4070 Ti AD104 [GeForce RTX 4070 Ti]	Nvidia	AD104	11,831,269	392,380	30.15	0 ^hrs 48 ^mins
4	GeForce RTX 3090 GA102 [GeForce RTX 3090]	Nvidia	GA102	10,110,494	415,139	24.35	0 ^hrs 59 ^mins
5	GeForce RTX 3090 Ti GA102 [GeForce RTX 3090 Ti]	Nvidia	GA102	9,881,344	412,274	23.97	1 ^hrs 0 ^mins
6	GeForce RTX 3080 Ti GA102 [GeForce RTX 3080 Ti]	Nvidia	GA102	8,162,203	384,864	21.21	1 ^hrs 8 ^mins
7	GeForce RTX 4070 AD104 [GeForce RTX 4070]	Nvidia	AD104	6,600,521	360,185	18.33	1 ^hrs 19 ^mins
8	GeForce RTX 3080 Lite Hash Rate GA102 [GeForce RTX 3080 Lite Hash Rate]	Nvidia	GA102	6,150,118	350,598	17.54	1 ^hrs 22 ^mins
9	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	6,132,572	350,757	17.48	1 ^hrs 22 ^mins
10	GeForce RTX 3080 GA102 [GeForce RTX 3080]	Nvidia	GA102	5,844,729	340,669	17.16	1 ^hrs 24 ^mins
11	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	5,732,022	69,415	82.58	0 ^hrs 17 ^mins
12	GeForce RTX 4060 Ti AD106 [GeForce RTX 4060 Ti]	Nvidia	AD106	5,297,930	332,746	15.92	1 ^hrs 30 ^mins
13	GeForce RTX 3070 Ti GA104 [GeForce RTX 3070 Ti]	Nvidia	GA104	4,921,988	324,757	15.16	1 ^hrs 35 ^mins
14	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	4,369,087	313,970	13.92	1 ^hrs 43 ^mins
15	Radeon RX 7900XT/XTX/GRE Navi 31 [Radeon RX 7900XT/XTX/GRE]	AMD	Navi 31	4,316,473	183,490	23.52	1 ^hrs 1 ^mins
16	GeForce RTX 4070 Max-Q / Mobile AD106M [GeForce RTX 4070 Max-Q / Mobile]	Nvidia	AD106M	4,302,127	312,070	13.79	1 ^hrs 44 ^mins
17	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	3,836,510	302,270	12.69	1 ^hrs 53 ^mins
18	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	3,737,545	297,285	12.57	1 ^hrs 55 ^mins
19	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	3,580,225	295,032	12.14	1 ^hrs 59 ^mins

20	Radeon RX 6900 XT Navi 21 [Radeon RX 6900 XT]	AMD	Navi 21	3,501,481	292,015	11.99	2 ^hrs 0 ^mins
21	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	3,191,766	283,454	11.26	2 ^hrs 8 ^mins
22	GeForce RTX 3060 Ti Lite Hash Rate GA104 [GeForce RTX 3060 Ti Lite Hash Rate]	Nvidia	GA104	3,140,549	281,556	11.15	2 ^hrs 9 ^mins
23	GeForce RTX 4060 AD107 [GeForce RTX 4060]	Nvidia	AD107	3,035,231	268,535	11.30	2 ^hrs 7 ^mins
24	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,741,585	269,809	10.16	2 ^hrs 22 ^mins
25	GeForce RTX 2070 TU106 [GeForce RTX 2070]	Nvidia	TU106	2,717,830	269,353	10.09	2 ^hrs 23 ^mins
26	GeForce RTX 2060 12GB TU106 [GeForce RTX 2060 12GB]	Nvidia	TU106	2,632,244	265,721	9.91	2 ^hrs 25 ^mins
27	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,590,970	265,161	9.77	2 ^hrs 27 ^mins
28	GeForce RTX 3060 Lite Hash Rate GA106 [GeForce RTX 3060 Lite Hash Rate]	Nvidia	GA106	2,582,834	191,692	13.47	1 ^hrs 47 ^mins
29	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,578,953	102,939	25.05	0 ^hrs 57 ^mins
30	GeForce RTX 3060 Mobile / Max-Q GA106M [GeForce RTX 3060 Mobile / Max-Q]	Nvidia	GA106M	2,440,227	258,996	9.42	2 ^hrs 33 ^mins
31	GeForce RTX 3060 GA106 [GeForce RTX 3060]	Nvidia	GA106	2,346,746	255,422	9.19	2 ^hrs 37 ^mins
32	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	2,324,834	255,921	9.08	2 ^hrs 39 ^mins
33	Radeon RX 6800/6800XT/6900XT Navi 21 [Radeon RX 6800/6800XT/6900XT]	AMD	Navi 21	2,294,321	253,276	9.06	2 ^hrs 39 ^mins
34	GeForce RTX 2070 Mobile TU106BM [GeForce RTX 2070 Mobile]	Nvidia	TU106BM	2,156,110	249,294	8.65	2 ^hrs 46 ^mins
35	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	2,122,609	235,480	9.01	2 ^hrs 40 ^mins
36	Radeon RX 7700XT/7800XT Navi 32 [Radeon RX 7700XT/7800XT]	AMD	Navi 32	1,984,539	217,466	9.13	2 ^hrs 38 ^mins
37	GeForce RTX 2070 Mobile TU106M [GeForce RTX 2070 Mobile]	Nvidia	TU106M	1,677,739	231,132	7.26	3 ^hrs 18 ^mins
38	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,651,957	227,548	7.26	3 ^hrs 18 ^mins
39	RTX A2000 GA106 [RTX A2000]	Nvidia	GA106	1,462,514	220,171	6.64	3 ^hrs 37 ^mins

40	GeForce GTX 1660 Mobile TU116M [GeForce GTX 1660 Mobile]	Nvidia	TU116M	1,386,602	215,474	6.44	3 ^hrs 44 ^mins
41	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,337,553	145,904	9.17	2 ^hrs 37 ^mins
42	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,263,027	208,589	6.06	3 ^hrs 58 ^mins
43	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	1,247,796	207,452	6.01	3 ^hrs 59 ^mins
44	Radeon RX Vega 56/64 Vega 10 XL/XT [Radeon RX Vega 56/64]	AMD	Vega 10 XL/XT	1,236,629	208,055	5.94	4 ^hrs 2 ^mins
45	GeForce RTX 3080 12GB GA102 [GeForce RTX 3080 12GB]	Nvidia	GA102	1,156,756	206,200	5.61	4 ^hrs 17 ^mins
46	GeForce GTX 980 GM204 [GeForce GTX 980] 4612	Nvidia	GM204	930,325	188,353	4.94	4 ^hrs 52 ^mins
47	Radeon RX 6600/6600 XT/6600M Navi 23 XT-XL [Radeon RX 6600/6600 XT/6600M]	AMD	Navi 23 XT-XL	894,627	184,257	4.86	4 ^hrs 57 ^mins
48	GeForce GTX 1060 6GB GP106 [GeForce GTX 1060 6GB] 4372	Nvidia	GP106	777,600	69,415	11.20	2 ^hrs 9 ^mins
49	Radeon RX 7700S/7600(S) Navi 33 [Radeon RX 7700S/7600(S)]	AMD	Navi 33	679,601	179,123	3.79	6 ^hrs 20 ^mins
50	GeForce GTX 1650 TU116 [GeForce GTX 1650] 3091	Nvidia	TU116	673,840	151,162	4.46	5 ^hrs 23 ^mins
51	Radeon RX 6700/6700XT/6800M Navi 22 XT-XL [Radeon RX 6700/6700XT/6800M]	AMD	Navi 22 XT-XL	538,891	117,609	4.58	5 ^hrs 14 ^mins

Research: PROTEIN-BRUSH-POLYMER-SIMULATION Folding Project #12117

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 12117

GPU PPD Averages

Research: PROTEIN-BRUSH-POLYMER-SIMULATION Folding Project #12117

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages