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Hanyuan Xie

dblp:441/9868 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Graph learning · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
protein design
0.912025
CPSea: Large-scale cyclic peptide-protein complex dataset for machine learning in cyclic peptide design · NeurIPS 2025
Bioinformatics and computational biology › structural bioinformatics
protein structure
0.912025
CPSea: Large-scale cyclic peptide-protein complex dataset for machine learning in cyclic peptide design · NeurIPS 2025
Machine learning › Graph learning
protein structure prediction
0.312025
CPSea: Large-scale cyclic peptide-protein complex dataset for machine learning in cyclic peptide design · NeurIPS 2025

Methods — techniques the papers use, named apart from their topics

structure filtering · 1.7dataset curation · 1.7
YearPublicationVenuePosition
2025 CPSea: Large-scale cyclic peptide-protein complex dataset for machine learning in cyclic peptide design
abstract
Cyclic peptides exhibit better binding affinity and proteolytic stability compared to their linear counterparts. However, the development of cyclic peptide design models is hindered by the scarcity of data. To address this, we introduce **CPSea**(**C**yclic **P**eptide **Sea**), a dataset of 2.71 million cyclic peptide-receptor complexes, curated through systematic mining of the AlphaFold Database (AFDB). Our pipeline extracts compact domains from AFDB, identifies cyclization sites using the $\beta$-carbon (C$_\beta$) distance thresholds, and applies multi-stage filtering to ensure structure fidelity and binding compatibility. Compared with experimental data of cyclic peptides, CPSea shows similar distributions in metrics on structure fidelity and wet-lab compatibility. To our knowledge, CPSea is the largest cyclic peptide-receptor dataset to date, enabling end-to-end model training for the first time. The dataset also showcases the feasibility of simulating inter-chain interactions using intra-chain interactions, expanding available resources for machine-learning models on protein-protein interactions. The dataset and relevant scripts are accessible on GitHub ([https://github.com/YZY010418/CPSea](https://github.com/YZY010418/CPSea)).
Ziyi Yang 0011, Hanyuan Xie, Yinjun Jia, Xiangzhe Kong, Jiqing Zheng, Ziting Zhang, Yang Liu 0003, Lei Liu 0049, Yanyan Lan
NeurIPS2