Folding project #12115, PEPTIDE-CONFORMATION-MODELING research

Research section Research projects and references

Project #12115 overview

Project Summary AI Beta

This project looks at how the shape of short protein pieces affects their ability to stick together in long chains. These chains could be used as medicines, but they break down easily. By studying a special protein piece called Trpzip2, scientists hope to figure out how to make these chains stronger and more effective.

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: 142,096
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 various bodily functions.

Scientific: MedicineBiotechnology / Pharmacology

Proteins are complex molecules that perform a wide range of functions in living organisms. They are involved in processes such as transporting nutrients, building tissues, and fighting infections.

Brush Polymers

Polymeric materials with side chains resembling a brush.

Technical: MedicineBiotechnology / Materials Science

Brush polymers are a type of polymer where long chains (the backbone) have many short branches attached. These branches can interact with molecules in their surroundings, making them useful for things like drug delivery and creating coatings.

Peptides

Short chains of amino acids.

Scientific: MedicineBiotechnology / Pharmacology

Peptides are like short chains of building blocks called amino acids. They play important roles in the body, such as sending signals between cells and defending against infection.

Enzyme Degradation

The breakdown of molecules by enzymes.

Scientific: MedicineBiotechnology / Pharmacology

Enzyme degradation is the process where special proteins called enzymes break down other molecules. This can happen naturally in our bodies, but it can also be a problem if it causes unwanted breakdown of important substances.

Beta-Hairpin Peptide

A type of peptide with a specific folded structure.

Scientific: MedicineBiotechnology / Structural Biology

Beta-hairpin peptides are small proteins with a unique shape that resembles a hairpin. This shape is important for their function and how they interact with other molecules.

Beta-Sheet

A common secondary structure in proteins.

Scientific: MedicineBiotechnology / Structural Biology

Beta-sheets are flat structures formed by multiple protein strands linked together. They are a common feature in many important proteins and play a role in their stability and function.

Polymer Conformation

The 3D shape of a polymer chain.

Scientific: MedicineBiotechnology / Materials Science

Polymer conformation refers to how the long chains of molecules in a polymer are arranged in space. The shape can affect the polymer's properties and how it interacts with its surroundings.

Trpzip2

A model beta-hairpin peptide.

Technical: MedicineBiotechnology / Structural Biology

Trpzip2 is a short protein used as a model system to study how proteins fold and interact. Its simple structure makes it easy to understand and analyze.

15-mer Polymer System

A system consisting of 15 peptide units linked together.

Technical: MedicineBiotechnology / Materials Science

A 15-mer polymer system is a group of 15 peptide molecules connected together. This type of system can be used to study how the length and arrangement of peptides affect their properties.

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	7,562,400	320,293	23.61	1 ^hrs 1 ^mins
2	GeForce RTX 3090 Ti GA102 [GeForce RTX 3090 Ti]	Nvidia	GA102	7,396,484	323,834	22.84	1 ^hrs 3 ^mins
3	GeForce RTX 3080 Ti GA102 [GeForce RTX 3080 Ti]	Nvidia	GA102	7,133,842	320,627	22.25	1 ^hrs 5 ^mins
4	GeForce RTX 2080 Ti TU102 [GeForce RTX 2080 Ti] M 13448	Nvidia	TU102	5,425,920	55,977	96.93	0 ^hrs 15 ^mins
5	GeForce RTX 3080 GA102 [GeForce RTX 3080]	Nvidia	GA102	5,223,680	285,413	18.30	1 ^hrs 19 ^mins
6	GeForce RTX 3080 12GB GA102 [GeForce RTX 3080 12GB]	Nvidia	GA102	5,160,220	287,717	17.94	1 ^hrs 20 ^mins
7	GeForce RTX 2080 Ti Rev. A TU102 [GeForce RTX 2080 Ti Rev. A] M 13448	Nvidia	TU102	4,896,960	282,167	17.35	1 ^hrs 23 ^mins
8	GeForce RTX 3080 Lite Hash Rate GA102 [GeForce RTX 3080 Lite Hash Rate]	Nvidia	GA102	4,557,154	181,869	25.06	0 ^hrs 57 ^mins
9	TITAN V GV100 [TITAN V] M 12288	Nvidia	GV100	4,478,615	274,767	16.30	1 ^hrs 28 ^mins
10	GeForce RTX 3070 Ti GA104 [GeForce RTX 3070 Ti]	Nvidia	GA104	3,771,191	257,395	14.65	1 ^hrs 38 ^mins
11	Radeon RX 7900XT/XTX/GRE Navi 31 [Radeon RX 7900XT/XTX/GRE]	AMD	Navi 31	3,362,695	152,128	22.10	1 ^hrs 5 ^mins
12	RTX A4500 GA102GL [RTX A4500]	Nvidia	GA102GL	3,291,578	250,185	13.16	1 ^hrs 49 ^mins
13	GeForce RTX 4060 AD107 [GeForce RTX 4060]	Nvidia	AD107	3,107,708	243,554	12.76	1 ^hrs 53 ^mins
14	GeForce RTX 3070 GA104 [GeForce RTX 3070]	Nvidia	GA104	3,100,205	235,464	13.17	1 ^hrs 49 ^mins
15	GeForce RTX 3060 Ti GA104 [GeForce RTX 3060 Ti]	Nvidia	GA104	3,063,247	243,330	12.59	1 ^hrs 54 ^mins
16	GeForce RTX 2080 Super TU104 [GeForce RTX 2080 SUPER]	Nvidia	TU104	2,955,954	238,705	12.38	1 ^hrs 56 ^mins
17	GeForce RTX 2080 Rev. A TU104 [GeForce RTX 2080 Rev. A] 10068	Nvidia	TU104	2,834,965	234,239	12.10	1 ^hrs 59 ^mins
18	GeForce RTX 3060 Ti Lite Hash Rate GA104 [GeForce RTX 3060 Ti Lite Hash Rate]	Nvidia	GA104	2,669,139	225,817	11.82	2 ^hrs 2 ^mins
19	GeForce RTX 2070 SUPER TU104 [GeForce RTX 2070 SUPER] 8218	Nvidia	TU104	2,646,102	100,229	26.40	0 ^hrs 55 ^mins

20	GeForce RTX 2080 TU104 [GeForce RTX 2080]	Nvidia	TU104	2,539,114	225,913	11.24	2 ^hrs 8 ^mins
21	GeForce RTX 2060 TU104 [GeForce RTX 2060]	Nvidia	TU104	2,400,236	233,359	10.29	2 ^hrs 20 ^mins
22	GeForce GTX 1080 Ti GP102 [GeForce GTX 1080 Ti] 11380	Nvidia	GP102	2,238,341	218,288	10.25	2 ^hrs 20 ^mins
23	TITAN X GP102 [TITAN X] 6144	Nvidia	GP102	2,191,835	217,317	10.09	2 ^hrs 23 ^mins
24	GeForce RTX 2060 Super TU106 [GeForce RTX 2060 SUPER]	Nvidia	TU106	2,129,605	205,961	10.34	2 ^hrs 19 ^mins
25	GeForce RTX 2070 TU106 [GeForce RTX 2070]	Nvidia	TU106	2,070,155	210,722	9.82	2 ^hrs 27 ^mins
26	GeForce RTX 3060 Lite Hash Rate GA106 [GeForce RTX 3060 Lite Hash Rate]	Nvidia	GA106	1,962,834	207,918	9.44	2 ^hrs 33 ^mins
27	GeForce RTX 2060 12GB TU106 [GeForce RTX 2060 12GB]	Nvidia	TU106	1,960,552	208,260	9.41	2 ^hrs 33 ^mins
28	GeForce RTX 3060 Mobile / Max-Q GA106M [GeForce RTX 3060 Mobile / Max-Q]	Nvidia	GA106M	1,914,520	206,902	9.25	2 ^hrs 36 ^mins
29	Radeon RX 7700XT/7800XT Navi 32 [Radeon RX 7700XT/7800XT]	AMD	Navi 32	1,836,639	205,492	8.94	2 ^hrs 41 ^mins
30	GeForce RTX 3060 GA106 [GeForce RTX 3060]	Nvidia	GA106	1,793,602	202,505	8.86	2 ^hrs 43 ^mins
31	GeForce RTX 2070 Mobile TU106BM [GeForce RTX 2070 Mobile]	Nvidia	TU106BM	1,634,612	197,525	8.28	2 ^hrs 54 ^mins
32	GeForce RTX 2060 TU106 [Geforce RTX 2060]	Nvidia	TU106	1,610,437	170,661	9.44	2 ^hrs 33 ^mins
33	GeForce GTX 1660 SUPER TU116 [GeForce GTX 1660 SUPER]	Nvidia	TU116	1,338,455	141,943	9.43	2 ^hrs 33 ^mins
34	GeForce RTX 2060 Mobile TU106M [GeForce RTX 2060 Mobile]	Nvidia	TU106M	1,303,446	176,666	7.38	3 ^hrs 15 ^mins
35	RTX A2000 GA106 [RTX A2000]	Nvidia	GA106	1,234,737	179,376	6.88	3 ^hrs 29 ^mins
36	GeForce GTX 1080 GP104 [GeForce GTX 1080] 8873	Nvidia	GP104	1,233,535	178,755	6.90	3 ^hrs 29 ^mins
37	RTX A2000 12GB GA106 [RTX A2000 12GB]	Nvidia	GA106	1,070,070	171,109	6.25	3 ^hrs 50 ^mins
38	GeForce GTX 1070 GP104 [GeForce GTX 1070] 6463	Nvidia	GP104	1,021,387	165,773	6.16	3 ^hrs 54 ^mins
39	GeForce GTX 980 Ti GM200 [GeForce GTX 980 Ti] 5632	Nvidia	GM200	998,847	165,508	6.04	3 ^hrs 59 ^mins

40	TITAN Xp GP102 [TITAN Xp] 12150	Nvidia	GP102	840,134	153,864	5.46	4 ^hrs 24 ^mins
41	GeForce GTX 980 GM204 [GeForce GTX 980] 4612	Nvidia	GM204	643,665	144,014	4.47	5 ^hrs 22 ^mins
42	GeForce GTX 1660 TU116 [GeForce GTX 1660]	Nvidia	TU116	575,186	136,024	4.23	5 ^hrs 41 ^mins
43	GeForce GTX 1650 TU116 [GeForce GTX 1650] 3091	Nvidia	TU116	521,696	137,077	3.81	6 ^hrs 18 ^mins
44	GeForce GTX 1650 Mobile / Max-Q TU117M [GeForce GTX 1650 Mobile / Max-Q]	Nvidia	TU117M	437,196	134,196	3.26	7 ^hrs 22 ^mins
45	GeForce GTX Titan Z GK110 [GeForce GTX Titan Z] 8122	Nvidia	GK110	366,323	125,100	2.93	8 ^hrs 12 ^mins
46	GeForce GTX 1050 3 GB Max-Q GP107M [GeForce GTX 1050 3 GB Max-Q]	Nvidia	GP107M	240,010	104,098	2.31	10 ^hrs 25 ^mins
47	GeForce GTX 950 GM206 [GeForce GTX 950] 1572	Nvidia	GM206	213,059	99,825	2.13	11 ^hrs 15 ^mins
48	GeForce GTX 1050 LP GP107 [GeForce GTX 1050 LP] 1862	Nvidia	GP107	212,839	55,977	3.80	6 ^hrs 19 ^mins
49	GeForce GTX 1050 Ti GP107 [GeForce GTX 1050 Ti] 2138	Nvidia	GP107	194,959	110,427	1.77	13 ^hrs 36 ^mins
50	GeForce MX150 GP107M [GeForce MX150]	Nvidia	GP107M	103,034	78,463	1.31	18 ^hrs 17 ^mins
51	GeForce GT 1030 GP108 [GeForce GT 1030]	Nvidia	GP108	86,400	55,977	1.54	15 ^hrs 33 ^mins

Research: PEPTIDE-CONFORMATION-MODELING Folding Project #12115

Project Summary AI Beta

Project team

Work unit

Official Project Description

Hardware Performance for Project 12115

GPU PPD Averages

Research: PEPTIDE-CONFORMATION-MODELING Folding Project #12115

Project Summary AI Beta

Project team

Work unit

Related projects

GPU PPD Averages