Publications

^* denotes equal contribution.

Technical Reports

Protenix-v1: Toward High-Accuracy Open-Source Biomolecular Structure Prediction

Protenix Team et al.

bioRxiv, 2026

GitHub

PXDesign: Fast, Modular, and Accurate De Novo Design of Protein Binders

Milong Ren, Jinyuan Sun, Jiaqi Guan, Cong Liu, Chengyue Gong, et al.

bioRxiv, 2025

GitHub

Protenix: Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction

Xinshi Chen, Yuxuan Zhang, Chan Lu, Wenzhi Ma, Jiaqi Guan, Chengyue Gong, et al.

bioRxiv, 2025

Publications

Unified Modeling of 3D Molecular Generation via Atomic Interactions with PocketXMol

Xingang Peng, Ruihan Guo, Fenglin Guo, Ziyi Wang, Jiayu Sun, Jiaqi Guan, et al.

Cell, 2026

Group Ligands Docking to Protein Pockets

Jiaqi Guan^*, Jiahan Li^*, Xiangxin Zhou, Xingang Peng, et al.

ICLR, 2025

Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows

Xiangxin Zhou, Yi Xiao, Haowei Lin, Xinheng He, Jiaqi Guan, Yang Wang, et al.

ICLR, 2025

Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension

Jiahan Li, Tong Chen, Shitong Luo, Chaoran Cheng, Jiaqi Guan, Ruihan Guo, et al.

ICLR, 2025

Orientation-Aware Networks for Protein Structure Representation Learning

Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, et al.

RECOMB, 2025

Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design

Xiangxin Zhou, Jiaqi Guan, Yijia Zhang, Xingang Peng, Liang Wang, Jianzhu Ma.

NeurIPS, 2024

LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion

Jiaqi Guan, Xingang Peng, Peiqi Jiang, Yunan Luo, Jian Peng, Jianzhu Ma.

NeurIPS, 2023 Spotlight

DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design

Jiaqi Guan^*, Xiangxin Zhou^*, Yuwei Yang, Yu Bao, Jian Peng, et al.

ICML, 2023

MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation

Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma.

ICML, 2023

3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction

Jiaqi Guan^*, Wesley Wei Qian^*, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma.

ICLR, 2023

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma.

ICML, 2022

Equivariant Point Cloud Analysis via Learning Orientations for Message Passing

Shitong Luo^*, Jiahan Li^*, Jiaqi Guan^*, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma.

CVPR, 2022 Oral

Energy-Inspired Molecular Conformation Optimization

Jiaqi Guan^*, Wesley Wei Qian^*, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng.

ICLR, 2022

A 3D Generative Model for Structure-Based Drug Design

Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng.

NeurIPS, 2021

Generative Hybrid Representations for Activity Forecasting with No-Regret Learning

Jiaqi Guan, Ye Yuan, Kris M. Kitani, Nicholas Rhinehart.

CVPR, 2020 Oral

A Method for Generating Synthetic Electronic Medical Record Text

Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang.

In IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019

Generation of Synthetic Electronic Medical Record Text

Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang.

In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, 2018

Energy-efficient Amortized Inference with Cascaded Deep Classifiers

Jiaqi Guan, Yang Liu, Qiang Liu, Jian Peng.

IJCAI, 2018