Evidence map›Paper›PMID 42399444›Full record

Reviewnpj drug discovery2026

Generative AI for controllable protein sequence design: A survey.

Yiheng Zhu, Zitai Kong, Jialu Wu, Mingze Yin, Weize Liu, Yuqiang Han, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu

Abstract readReview
In one paragraph

Review in npj drug discovery, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Yiheng ZhuZhongguancun Academy, Beijing, China.
Zitai KongZhejiang University, College of Computer Science and Technology, Hangzhou, China.
Jialu WuZhejiang University, College of Pharmaceutical Sciences, Hangzhou, China.
Mingze YinZhejiang University, College of Computer Science and Technology, Hangzhou, China.
Weize LiuZhejiang University, Polytechnic Institute, Hangzhou, China.
Yuqiang HanZhejiang University, College of Computer Science and Technology, Hangzhou, China.
Hongxia XuZhejiang University School of Medicine, The Second Affiliated Hospital and Liangzhu Laboratory, Hangzhou, China.
Chang-Yu HsiehZhejiang University, College of Pharmaceutical Sciences, Hangzhou, China. kimhsieh@zju.edu.cn.
Tingjun HouZhejiang University, College of Pharmaceutical Sciences, Hangzhou, China. tingjunhou@zju.edu.cn.
Jian WuZhejiang University School of Medicine, The Second Affiliated Hospital and Liangzhu Laboratory, Hangzhou, China. wujian2000@zju.edu.cn.

Funding

Huadong Medicine Joint Fund of 714 Zhejiang Provincial Natural Science Foundation of China LHDMZ25H300001National Natural Science Foundation of China 22373085Zhejiang Key 711 Laboratory of Medical Imaging Artificial Intelligence, State Key Laboratory of Transvascular Implantation Devices SKLTID2024003Zhejiang Key R&D Program of China 2024C03048
6 · The paper itself

Abstract

The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial search space remains a severe challenge due to time and financial constraints. This scenario is rapidly evolving as the transformative advancements in AI have been propelling the protein design field into a new era. In this survey, we systematically review recent advances in generative AI for controllable protein sequence design. To set the stage, we first outline the foundational tasks in protein sequence design in terms of the constraints involved and present key generative models and optimization algorithms. We then offer in-depth reviews of each design task and discuss the in silico evaluation approaches and pertinent applications. Finally, we identify the unresolved challenges and highlight research opportunities that merit deeper exploration.

Identifiers

PMID42399444
PMCPMC13332047

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.