Peptide Design Competition-Frontiers In Biological Structures

Peptide Design Competition

Round 1

The Peptide Design Competition (PDC) is trying to design a new drug for diseases like obesity and diabetes.

Example

Competition Prizes

Gold medalist

¥35,000

One first prize
The prize is equivalent to

$5,000

Silver medalist

¥14,000

Two second prizes
The prize is equivalent to

$2,000

Bronze medalist

¥7,000

Three third prizes
The prize is equivalent to

$1,000

Leaderboard

download(Excel/CSV)

Rank	First Name	Last Name	Team Name	Peptide Name	All Methods	Amino acid Sequence	iptm AB((NK2R Peptide))	iptm AD((NK2R NKA))	Synthesize	Chain Iptm	chain pair iptm	chain pair pae min	chain ptm	fraction disordered	iptm	ptm	ranking score	mean plddt CA all	mean plddt CA chainB
1	C	CCC	OneShotOnly_c1	7	BindCraft	HCWEGATMM	0.95	0.14	1	[0.6, 0.54, 0.5, 0.09]	[[0.76, 0.95, 0.71, 0.14], [0.95, 0.03, 0.67, 0.0], [0.71, 0.67, 0.64, 0.13], [0.14, 0.0, 0.13, 0.01]]	[[0.76, 1.2, 1.32, 20.86], [1.4, 0.76, 5.02, 22.1], [1.33, 4.48, 0.76, 21.43], [23.36, 29.85, 23.62, 0.77]]	[[0.76, 1.2, 1.32, 20.86], [1.4, 0.76, 5.02, 22.1], [1.33, 4.48, 0.76, 21.43], [23.36, 29.85, 23.62, 0.77]]	0.18	0.7	0.72	0.79	78.46235825	89.44222222
2	C	CCC	OneShotOnly_c1	8	BindCraft	WRFYPKM	0.95	0.31	1	[0.66, 0.54, 0.57, 0.21]	[[0.77, 0.95, 0.73, 0.31], [0.95, 0.03, 0.67, 0.0], [0.73, 0.67, 0.65, 0.32], [0.31, 0.0, 0.32, 0.01]]	[[0.76, 1.27, 1.28, 14.46], [1.48, 0.76, 5.16, 17.96], [1.3, 4.49, 0.76, 14.66], [22.85, 29.98, 15.4, 0.77]]	[[0.76, 1.27, 1.28, 14.46], [1.48, 0.76, 5.16, 17.96], [1.3, 4.49, 0.76, 14.66], [22.85, 29.98, 15.4, 0.77]]	0.18	0.72	0.73	0.81	79.01682171	89.59857143
3	RollTheDice	I	RollTheDice	G0001	Custom evolutionary algorithm	CFYFLM	0.95	0.11	1	[0.59, 0.54, 0.49, 0.07]	[[0.76, 0.95, 0.71, 0.11], [0.95, 0.03, 0.66, 0.0], [0.71, 0.66, 0.64, 0.11], [0.11, 0.0, 0.11, 0.01]]	[[0.76, 1.32, 1.38, 24.54], [1.58, 0.76, 5.24, 25.14], [1.38, 4.56, 0.76, 24.1], [26.17, 30.83, 23.49, 0.77]]	[[0.76, 1.32, 1.38, 24.54], [1.58, 0.76, 5.24, 25.14], [1.38, 4.56, 0.76, 24.1], [26.17, 30.83, 23.49, 0.77]]	0.16	0.7	0.72	0.79	78.47983182	89.52333333
4	RollTheDice	I	RollTheDice	G0095	Custom evolutionary algorithm	YCMEAAKMM	0.95	0.14	1	[0.6, 0.55, 0.51, 0.09]	[[0.76, 0.95, 0.72, 0.14], [0.95, 0.03, 0.69, 0.0], [0.72, 0.69, 0.65, 0.13], [0.14, 0.0, 0.13, 0.01]]	[[0.76, 1.21, 1.25, 20.87], [1.37, 0.76, 4.38, 21.93], [1.29, 4.37, 0.76, 21.36], [22.61, 29.79, 23.08, 0.77]]	[[0.76, 1.21, 1.25, 20.87], [1.37, 0.76, 4.38, 21.93], [1.29, 4.37, 0.76, 21.36], [22.61, 29.79, 23.08, 0.77]]	0.18	0.71	0.73	0.8	78.65354381	89.52444444
5	RollTheDice	I	RollTheDice	G0092	Custom evolutionary algorithm	HCSEAAKMM	0.95	0.14	1	[0.6, 0.55, 0.52, 0.09]	[[0.76, 0.95, 0.72, 0.14], [0.95, 0.03, 0.7, 0.0], [0.72, 0.7, 0.65, 0.13], [0.14, 0.0, 0.13, 0.01]]	[[0.76, 1.22, 1.24, 20.78], [1.37, 0.76, 4.34, 21.91], [1.26, 4.25, 0.76, 21.47], [22.61, 29.86, 23.3, 0.77]]	[[0.76, 1.22, 1.24, 20.78], [1.37, 0.76, 4.34, 21.91], [1.26, 4.25, 0.76, 21.47], [22.61, 29.86, 23.3, 0.77]]	0.18	0.71	0.73	0.81	78.88204897	89.35666667
6	RollTheDice	I	RollTheDice	G0016	Custom evolutionary algorithm	YCSEAAKMM	0.95	0.14	1	[0.6, 0.55, 0.52, 0.09]	[[0.76, 0.95, 0.73, 0.14], [0.95, 0.03, 0.7, 0.0], [0.73, 0.7, 0.65, 0.13], [0.14, 0.0, 0.13, 0.01]]	[[0.76, 1.19, 1.23, 20.79], [1.35, 0.76, 4.34, 21.84], [1.26, 4.23, 0.76, 21.45], [22.69, 29.9, 23.3, 0.77]]	[[0.76, 1.19, 1.23, 20.79], [1.35, 0.76, 4.34, 21.84], [1.26, 4.23, 0.76, 21.45], [22.69, 29.9, 23.3, 0.77]]	0.18	0.72	0.73	0.81	79.12359536	89.86111111
7	RollTheDice	I	RollTheDice	G0094	Custom evolutionary algorithm	CFWTIM	0.95	0.25	1	[0.64, 0.54, 0.55, 0.18]	[[0.76, 0.95, 0.72, 0.25], [0.95, 0.03, 0.67, 0.0], [0.72, 0.67, 0.64, 0.27], [0.25, 0.0, 0.27, 0.01]]	[[0.76, 1.33, 1.36, 16.85], [1.53, 0.76, 5.83, 20.09], [1.35, 4.46, 0.76, 16.26], [22.58, 30.5, 16.71, 0.77]]	[[0.76, 1.33, 1.36, 16.85], [1.53, 0.76, 5.83, 20.09], [1.35, 4.46, 0.76, 16.26], [22.58, 30.5, 16.71, 0.77]]	0.16	0.71	0.72	0.79	78.47425614	90.93
8	RollTheDice	I	RollTheDice	G0087	Custom evolutionary algorithm	ERFYPRM	0.95	0.32	1	[0.66, 0.54, 0.58, 0.22]	[[0.77, 0.95, 0.73, 0.32], [0.95, 0.03, 0.68, 0.0], [0.73, 0.68, 0.64, 0.33], [0.32, 0.0, 0.33, 0.01]]	[[0.76, 1.27, 1.29, 13.85], [1.54, 0.76, 5.39, 17.04], [1.28, 4.39, 0.76, 14.19], [22.84, 29.95, 15.19, 0.77]]	[[0.76, 1.27, 1.29, 13.85], [1.54, 0.76, 5.39, 17.04], [1.28, 4.39, 0.76, 14.19], [22.84, 29.95, 15.19, 0.77]]	0.18	0.72	0.73	0.81	78.99125323	89.77428571
9	Anji	Liu	C341-team	1	ProteinMPNN/LigandMPNN	ICWEGATMM	0.95	0.13	1	[0.6, 0.54, 0.51, 0.09]	[[0.76, 0.95, 0.72, 0.13], [0.95, 0.03, 0.68, 0.0], [0.72, 0.68, 0.64, 0.13], [0.13, 0.0, 0.13, 0.01]]	[[0.76, 1.24, 1.27, 21.27], [1.45, 0.76, 4.96, 22.74], [1.29, 4.45, 0.76, 21.85], [23.06, 30.16, 23.28, 0.77]]	[[0.76, 1.24, 1.27, 21.27], [1.45, 0.76, 4.96, 22.74], [1.29, 4.45, 0.76, 21.85], [23.06, 30.16, 23.28, 0.77]]	0.18	0.71	0.72	0.8	78.81153351	89.63
10	Anji	Liu	C341-team	2	ProteinMPNN/LigandMPNN	QCWEGATMM	0.95	0.14	1	[0.6, 0.54, 0.51, 0.09]	[[0.76, 0.95, 0.71, 0.14], [0.95, 0.03, 0.68, 0.0], [0.71, 0.68, 0.64, 0.13], [0.14, 0.0, 0.13, 0.01]]	[[0.76, 1.26, 1.31, 21.0], [1.46, 0.76, 5.05, 22.17], [1.3, 4.5, 0.76, 21.4], [22.88, 30.18, 23.4, 0.77]]	[[0.76, 1.26, 1.31, 21.0], [1.46, 0.76, 5.05, 22.17], [1.3, 4.5, 0.76, 21.4], [22.88, 30.18, 23.4, 0.77]]	0.18	0.7	0.72	0.8	79.19197165	90.39222222

Competition Details

Scientific Background

• Problem: There's a global rise in metabolic diseases. An ideal treatment would both reduce food intake and increase energy expenditure. Current drugs often fail to do both effectively and safely.

• Proposed Target: The Neurokinin-2 Receptor (NK2R, Uniprot ID: P21452) is identified as a promising target because it has a unique dual action:

- Centrally (in the nervous system): It suppresses appetite.

- Peripherally (in body tissues): It increases energy expenditure.

• The Challenge: The body's natural activator for NK2R, Neurokinin A (NKA), cannot be used as a drug for two main reasons:

1.Extremely Short Half-life: It breaks down in the body within minutes.

2.Lack of Selectivity: It activates other receptors (NK1R and NK3R), with NK1R activation leading to serious side effects like CNS disorders, inflammation, and pain.

Competition Goal

The main objective is to design highly selective and high-affinity NK2R peptide agonists. The designed molecule should:

• Maximize the benefits of activating NK2R.

• Avoid the side effects from activating other receptors, especially NK1R.

Peptide Submission Rules

1) The maximum length of the submitted sequence does not exceed 40 natural amino acids, and the similarity with the natural peptide sequence is < 30%. The natural NKA peptide sequence is: HKTDSFVGLM, and the similarity is calculated using mmseqs2.

2) We will use AlphaFold3 to perform structural predictions on the submitted peptide sequences against the target NK2R and the naturally activating peptide NKA. We will only synthesize and test the top 100 sequences in terms of predicted parameters (ipTM, ipAE, etc.) if the submitted sequences can compete out NKA from the binding pocket. Protein sequences: NK2R, NK1R, Gα

3) The evaluation metric for the first round is activity, specifically EC50_[NK2R].

4) The evaluation metrics for the second round include both activity and selectivity. The metric for selectivity is EC50_[NK2R]/EC50_[NK1R]. When EC50_[NK2R] < 100 nM, priority is given to selectivity; when EC50_[NK2R] > 100 nM, priority is given to activity. Assuming the EC50_[NK2R] of both Sequence A and Sequence B is less than 100 nM, the calculation formula at this stage is: Z_[activity] + 2.0 * Z_{[selectivity]}, where Z represents the normalized score (based on experimental results of all tested sequences).

5) Please pay special attention: all sequences and data submitted in this competition will be open for sharing and can be used by others free of charge.

Competition Schedule

2025.08.18-2025.09.30 - Submit the designed peptide sequences of the first round.

2025.10.01-2025.11.14 - Synthesize peptide sequences and test their activity of the first round.

2025.11.15-2025.12.15 - Submit the designed peptide sequences of the second round.

2025.12.16-2026.02.28 - Synthesize peptide sequences and test their activity of the second round.

2026.03 - Announce the final results.

Chinese participants: You can add the official WeChat account (FRCBS-THU) to enter the competition discussion group.

Foreign participants: You can click on the link to enter the Discord group.

Organizing Committee

Boxue Tian

Jianzhu Ma

Yafei Yuan

Xiangyu Liu

Scientific Advisory Board

Yigong Shi

Hongwei Wang

Xinquan Wang

Haitao Li

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