Protein Design Labs

🤩 Welcome to our curated list of computational protein design research labs!

This list serves as a public reference for labs engaged in computational protein design research. While we've made every effort to be comprehensive, our knowledge may be limited (mostly limited to labs in the US and China).

We apologize if we've missed your lab or labs you're familiar with. Suggestions for additions are highly welcomed – please feel free to open new issues.

📝 Note: The list was based on @Zuricho's post on Zhihu in Chinese. The current version has been expanded and formatted with the assistance of @Leo-T-Zang.

Table of Contents

• #North America
  • 🇺🇸 United States
    • MIT
    • Harvard University
    • Stanford University
    • University of Washington
    • UCSF
    • UC Berkeley
    • UCLA
    • Caltech
    • University of Chicago
    • UIUC
    • Scripps Research Institute
    • Princeton University
    • Duke University
    • John Hopkins University
    • Carnegie Mellon University
    • Northwestern University
    • UNC Chapel Hill
    • St. Jude Children’s Research Hospital
    • Dartmouth College
    • Columbia University
    • New York University
    • Northeastern University
    • Texas A&M University
    • UCSB
    • UCSC
    • UT Southwestern
    • University of Wisconsin-Madison
    • University of Alabama at Birmingham
    • University of Florida
    • Georgia Institute of Technology
    • University of Delaware
    • Wake Forest University
    • Vanderbilt University
  • 🇨🇦 Canada
    • Mila - Quebec AI Institute
    • University of Toronto
• #EMEA
  • 🇬🇧 United Kingdom
    • University of Cambridge
    • University of Oxford
    • Imperial College London
    • UCL
    • University of Edinburgh
    • University of Bristol
    • Cardiff University
    • University of Leeds
  • 🇮🇪 Ireland
    • University College Cork
  • 🇨🇭 Switzerland
    • ETH Zurich
    • EPFL
  • 🇩🇪 Germany
    • TUM
    • FU Berlin
    • Leipzig University
    • University of Bayreuth
  • 🇫🇷 France
    • Ecole Polytechnique
    • INRAE MIAT
    • Toulouse Biotechnology Institute
  • 🇪🇸 Spain
    • Centre for Genomic Regulation
    • IBMB CSIC
    • IMDEA Nanoscience research institute
    • Barcelona Supercomputing Center
    • Spanish National Research Council
    • Universitat Autònoma de Barcelona
  • 🇦🇹 Austria
    • TU Graz
  • 🇧🇪 Belgium
    • Vrije Universiteit Brussel
  • 🇸🇪 Sweden
    • Stockholm University
  • 🇩🇰 Denmark
    • University of Copenhagen
    • Aarhus University
  • 🇮🇱 Israel
    • Weizmann Institute of Science
    • Tel Aviv University
  • 🇸🇦 Saudi Arabia
    • KAUST
    • Mohamed bin Zayed University of AI
  • 🇳🇱 Netherlands
    • Eindhoven University of Technology
• #Asia
  • 🇯🇵 Japan
    • Tokyo University
  • 🇸🇬 Singapore
    • National University of Singapore
  • 🇰🇷 South Korea
    • Seoul National University
    • KAIST
    • POSTECH
    • IBS
  • 🇭🇰 Hong Kong
    • Chinese University of Hong Kong
    • HKUST
  • 🇨🇳 China Mainland
    • Peking University 北京大学
    • Tsinghua University 清华大学
    • CAS ICT 中国科学院计算技术研究所
    • CAS IBP 中国科学院生物物理研究所
    • Renmin University of China 中国人民大学
    • Shanghai Jiao Tong University 上海交通大学
    • Fudan University 复旦大学
    • ShanghaiTech University 上海科技大学
    • CAS SIMM 中国科学院上海药物研究所
    • CAS CEMCS 中国科学院分子细胞科学卓越创新中心
    • Zhejiang University 浙江大学
    • Westlake University 西湖大学
    • Zhejiang University of Technology 浙江工业大学
    • Sun Yat-sen University 中山大学
    • CAS SIAT 深圳先进技术研究院
    • Tsinghua SIGS 清华大学深圳国际研究生院
    • SUSTech 南方科技大学
    • USTC 中国科学技术大学
    • Xiamen University 厦门大学
    • Shandong University 山东大学
    • CAS TIB 中国科学院天津工业生物技术研究所

#North America

🇺🇸 United States

MIT

Bonnie Berger

• Lab website: Link

Tommi S. Jaakkola

• Lab website: Link

Regina Barzilay

• Lab website: Link
• Related paper:
  • CLIPZyme: arXiv:2402.06748

Tess E. Smidt

• Lab website: Link

Sergey Ovchinnikov

• Lab website: Link

Alexandre Rives

• Lab website: NA
• Related papers:
  • ESM3
  • ESMFold
  • ESM

Amy E. Keating

• Lab website: Link

James J. Collins

• Lab website: Link

Harvard University

Debora Marks & Chris Sander

• Lab websites:
  • Debbie Marks Lab
  • Sander Lab
• Related papers:
  • CoVES
  • ProteinGym
  • Evolutionary Couplings

Nicholas F. Polizzi

• Lab website: Polizzi Lab

Marinka Zitnik

• Lab website: Link

George Church

• Lab website: Link

Yilun Du

• Lab website: Link

Omar Abudayyeh & Jonathan Gootenberg

• Lab website: Link

Stanford University

Possu Huang

• Lab website: Link

Jure Leskovec

• Lab website: Link

Rhiju Das

• Lab website: Link

Brian Trippe

• Lab website: Link

Brian Hie

• Lab website: Link

Ron Dror

• Lab website: Link

James Zou

• Lab website: Link

University of Washington

David Baker

• Lab website: Baker Lab - UW Institute for Protein Design
• Research focus: Protein design

Neil King

• Lab website: King Lab | Research
• Research focus: Protein nanomaterial design for medicine, self-assembling protein nanomaterial design

Gaurav Bhardwaj

• Lab website: Bhardwaj Lab
• Research focus: Peptide design for therapeutics

Frank Dimaio

• Lab website: DiMaio Lab - University of Washington
• Research focus: Protein structure determination from low-resolution experimental data

UCSF

William DeGrado

• Lab website: Link

Tanja Kortemme

• Lab website: Link

UC Berkeley

Jennifer Doudna

• Lab website: Link

Yun S. Song

• Personal website: Yun S. Song

Jennifer Listgarten

• Personal website: Jennifer Listgarten

Pieter Abbeel

• Lab website: Link

UCLA

Quanquan Gu

• Lab website: Link
• Personal website: Quanquan Gu
• Related papers:
  • LM-design
  • DPLM

Lin Jiang

• Personal website: Lin Jiang, Ph.D.

Caltech

Frances Arnold

• Lab website: Link

Steve Mayo

• Lab website: Welcome to the Mayo Group

Yisong Yue

• Lab website: Link

University of Chicago

Rama Ranganathan

• Lab website: Ranganathan Lab
• Related paper:
  • Evolution-based design

Andrew Ferguson

• Lab website: Ferguson Lab
• Personal website: Andrew Ferguson
• Related paper:
  • SH3 design

UIUC

Huimin Zhao

• Lab website: Zhao Group @ UIUC

Ge Liu

• Personal website: Ge Liu

Scripps Research Institute

William E. Balch

• Lab website: Balch Lab

Marco Mravic

• Lab website: Mravic Lab

Princeton University

Mengdi Wang

• Lab website: Link

Ellen D. Zhong

• Lab website: Link

Duke University

Bruce Donald

• Lab website: Link

Pranam D. Chatterjee

• Lab website: Link

Alexander Tong

• Lab website: Link

Philip A. Romero

• Lab website: Link

Rohit Singh

• Lab website: Link

David C. Richardson & Jane Shelby Richardson

• Lab website: Link

John Hopkins University

Jeffrey J. Gray

• Lab website: Link

Carnegie Mellon University

Lei Li

• Personal website: Lei LI
• Related papers:
  • SurfPro
  • EnzyGen

Northwestern University

Gabriel J. Rocklin

• Lab website: Link

Neha P. Kamat

• Lab website: Link
• Related Papers:
  • Protein-lipid interaction engineerning

UNC Chapel Hill

Brian Kuhlman

• Lab website: Kuhlman Lab

Tianlong Chen

• Personal website: Tianlong Chen

Huaxiu Yao

• Personal website: Huaxiu Yao's Personal Website

Huong Kratochvil

• Lab website: Link

St. Jude Children’s Research Hospital

Elizabeth H. Kellogg

• Lab website: link

Dartmouth College

Gevorg Grigoryan (Left for Company)

• Personal website: Gevorg Grigoryan

Columbia University

Mohammed AlQuraishi

• Lab website: AlQuraishi Lab at Columbia University

Scott Banta

• Lab website: Banta Lab

Anum Glasgow

• Personal website: Anum Glasgow

New York University

Jin Kim Montclare

• Lab website: Montclare Lab

Kyunghyun Cho

• Lab website: Link
• Related paper:
  • Protein Design w/ Guided Discrete Diffusion

Andrew Gordon Wilson

• Lab website: Link
  • Protein Design w/ Guided Discrete Diffusion

Northeastern University

Wengong Jin

• Personal website: Wengong Jin

Texas A&M University

Shuiwang Ji

• Personal website: Shuiwang Ji

UCSB

Yang Yang

• Lab website: Yang Lab at UCSB

UCSC

Andy Hsien-Wei Yeh

• Lab website: Link
• Related paper: bioRxiv 2023

UT Southwestern

Qian Cong

• Lab website: Link

University of Wisconsin-Madison

Anthony Gitter

• Lab website: Link

University of Alabama at Birmingham

Hy Truong Son

• Lab website: Link

University of Florida

Wenjun Xie

• Lab website: Link

Georgia Institute of Technology

Yunan Luo

• Lab website: Link

University of Delaware

Jason Gleghorn

• Lab website: Link

Wake Forest University

Katherine I. Albanese

• Lab website: Link

Vanderbilt University

Zhongyue Yang

• Lab website: Link

Jens Meiler

• Lab website: Link

Stephanie Wankowicz

• Lab website: Link

Hassane Mchaourab

• Lab website: Link

Ben Brown

• Lab website: Link

AI for Protein Dynamics Center

• Lab website: Link

🇨🇦 Canada

Mila - Quebec AI Institute

Yoshua Bengio

• Lab website: Link

Jian Tang

• Lab website: Link

University of Toronto

Philip M. Kim

• Lab website: Link

#EMEA

🇬🇧 United Kingdom

University of Cambridge

Pietro Liò

• Lab website: Link

University of Oxford

Michael Bronstein

• Lab website: Link

Charlotte Deane

• Lab website: OPIG

Yarin Gal

• Lab website: Yarin Gal - Home Page | Oxford Machine Learning

Imperial College London

Guang Yang

• Lab website: link

UCL

David T. Jones

• Lab website: Link

University of Edinburgh

Chris Wells Wood

• Lab website: Link

Lynne Regan

• Lab website: Link

University of Bristol

Dek Woolfson

• Lab website: Link

Ross Anderson

• Lab website: Link

Cardiff University

Fabio Parmeggiani

• Lab website: Link
• Related papers:
  • Repeat protein design

University of Leeds

Darren Tomlinson

• Lab website: Link

Takashi Ochi

• Lab website: Link

Neil Ranson

• Lab website: Link

Richard Bayliss

• Lab website: Link

David Brockwell

• Lab website: Link

Sheena Radford

• Lab website: Link

🇮🇪 Ireland

University College Cork

Sabin Tabirca

• Lab website: Link

🇨🇭 Switzerland

ETH Zurich

Donald Hilvert

• Lab website: Hilvert Lab
• Related paper: Design from peptide

EPFL

Bruno E. Correia

• Lab website: Link

Anne-Florence Bitbol

• Lab website: Bitbol Lab

🇩🇪 Germany

TUM

Rost Burkhard

• Lab website: Rost Lab

FU Berlin

Frank Noé

• Lab website: Link

Leipzig University

Clara T. Schoeder

• Lab website: Link
• Related paper:
  • Combine Rosetta and ESM

University of Bayreuth

Birte Höcker

• Lab website: Link

🇫🇷 France

Ecole Polytechnique

Thomas Simonson

• Lab website: Link
• Related paper:
  • Proteus

INRAE MIAT

Thomas Schiex

• Lab website: Link

Toulouse Biotechnology Institute

Sophie Barbe

🇪🇸 Spain

Centre for Genomic Regulation

Noelia Ferruz

• Lab website: Artificial Intelligence for Protein Design - Noelia Ferruz lab
• Related paper:
  • ZymCTRL

IBMB CSIC

Enrique Marcos

• Lab website: Link
• Related paper:
  • de novo immunoglobulin design

IMDEA Nanoscience research institute

Sara H Mejias

• Lab website: Link

Barcelona Supercomputing Center

Victor Guallar Tasies

• Lab website: Link

Spanish National Research Council

Manuel Ferrer Martínez

• Lab website: Link

Universitat Autònoma de Barcelona

Salvador Ventura Zamora

• Lab website: Link

🇦🇹 Austria

TU Graz

Gustav Oberdorfer

• Lab website: Link
• Related Paper:
  • Helical Bundle design
  • ESM-Scan

🇧🇪 Belgium

Vrije Universiteit Brussel

Anastassia A. Vorobieva

• Lab website: Link
• Related papers:
  • Nanopore design

🇸🇪 Sweden

Stockholm University

Patrick Bryant

• Lab website: Link
• Related papers:
  • EvoBind for binder design

🇩🇰 Denmark

University of Copenhagen

Kresten Lindorff-Larsen

• Lab website: Link
• Related papers:
  • IDP design

Martin Willemoës

• Lab website: Link
• Related papers:
  • Glycoside hydrolase carving-out

Aarhus University

Michael Westberg

• Lab website: Link

🇮🇱 Israel

Weizmann Institute of Science

Sarel J Fleishman

• Lab website: Link
• Related papers:
  • CADENZ
  • Antibody humanness optimize
  • Peroxidases Design
  • Enzyme Repertoires design

Tel Aviv University

Jérôme Tubiana

• Lab website: Link

🇸🇦 Saudi Arabia

KAUST

Xin Gao

• Lab website: Link

Mohamed bin Zayed University of AI

Eric Xing

• Lab website: Link

🇳🇱 Netherlands

Eindhoven University of Technology

Francesca Grisoni

• Lab website: Link

#Asia

🇯🇵 Japan

Tokyo University

Kotaro Tsuboyama

• Lab website: Link
• Related papers:
  • Mega-scale mutation scanning

🇸🇬 Singapore

National University of Singapore

Yang Zhang

• Research focus: Structure prediction
• Lab website: The Yang Zhang Lab
• Related papers:
  • EvoDesign
  • EvoEF2

🇰🇷 South Korea

Seoul National University

Martin Steinegger

• Lab website: Link

Minkyung Baek

• Lab website: Link

KAIST

Ji-Joon Song

• Lab website: Link

Byung-Ha Oh

• Lab website: Link

POSTECH

Sangmin Lee

• Lab website: Link

IBS

Ho Min Kim

• Lab website: Link

🇭🇰 Hong Kong

Chinese University of Hong Kong

Yu Li

• Lab website: Link
• Related Paper:
  • Dense Homolog Retriever

HKUST

Danqing Zhu

• Lab website: Link
• Related Paper
  • AAV library design

🇨🇳 China Mainland

Peking University 北京大学

Luhua Lai 来鲁华

• Lab website: Link
• Related Papers:
  • [Angew 2024] GeoSeqBuilder: https://onlinelibrary.wiley.com/doi/10.1002/anie.202411461

Yi Qin Gao 高毅勤

• Lab website: Link

Chu Wang 王初

• Lab website: Link

Wentao Zhang 张文涛

• Lab website: Link
• Related Papers:
  • [ACL 2024] ProtLLM: ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training

Tsinghua University 清华大学

Haipeng Gong 龚海鹏

• Lab website: Link
• Related Papers:
  • [NatComm 2024] SPIRED: https://www.nature.com/articles/s41467-024-51776-x

Chunfu Xu 徐纯福

• Lab website: Link
• Related Papers:
  • [Nature 2020] Transmembrane pore design: https://www.nature.com/articles/s41586-020-2646-5

Jianzhu Ma 马剑竹

• Lab website: Link
• Related Papers:
  • [NeurlPS 2022] DiffAb: https://www.biorxiv.org/content/10.1101/2022.07.10.499510.abstract

Yang Liu 刘洋

• Lab website: Link
• Related Papers:
  • [ICLR 2023] Antibody design: https://arxiv.org/abs/2208.06073

Yanyan Lan 兰艳艳

• Lab website: Link

Hao Zhou 周浩

• Lab website: Link
• Related Papers:
  • [ICML 2024] ESM-AA: https://arxiv.org/abs/2403.12995

CAS ICT 中国科学院计算技术研究所

Dongbo Bu 卜东波

• Lab website: Link
• Related Papers:
  • [Nature Machine Intelligence 2024] CarbonDesign: https://www.nature.com/articles/s42256-024-00838-2

Haicang Zhang 张海仓

• Lab website: Link
• Related Papers:
  • [Nature Machine Intelligence 2024] CarbonDesign: https://www.nature.com/articles/s42256-024-00838-2

CAS IBP 中国科学院生物物理研究所

Xianen Zhang 张先恩

• Lab website: Link
• Related Papers:
  • ProT-Diff for AMP generation

Dianbing Wang 王殿冰

• Related Papers:
  • ProT-Diff for AMP generation

Renmin University of China 中国人民大学

Wenbing Huang 黄文炳

• Lab website: Link
• Related Papers:
  • Antibody design

Shanghai Jiao Tong University 上海交通大学

Liang Hong 洪亮

• Lab website: Link
• Related Papers:
  • CPDiffusion for Argonaute design
  • CPDiffusion-SS for secondary structure based design

Haifeng Cheng 陈海峰

• Lab website: Link
• Related Papers:
  • GPD
  • Sequence design benchmark

Shuangjia Zheng 郑双佳

• Lab website: Link

Yang Yang 杨旸

• Lab website: Link

Hongbin Shen 沈红斌

• Lab website: Link

Rui Qing 庆睿

• Lab website: Link
• Related Papers:
  • [NatComm 2024] QTY code: https://www.nature.com/articles/s41467-024-48513-9, [Chem Rev 2023] Review: https://pubs.acs.org/doi/full/10.1021/acs.chemrev.1c00757

Yuguang Wang 王宇光

• Lab website: Link
• Related Papers:
  • [NeurIPS 2023] GraDe-IF: https://arxiv.org/abs/2306.16819

Fudan University 复旦大学

Siqi Sun 孙思琦

• Lab website: Link

Jianpeng Ma 马剑鹏

• Lab website: Link
• Related Papers:
  • [bioRxiv 2024] https://www.biorxiv.org/content/10.1101/2024.08.20.608889v1.full

ShanghaiTech University 上海科技大学

Jiayi Dou 豆佳宜

• Lab website: Link
• Related Papers:
  • [Nature 2018] β-barrel design: https://www.nature.com/articles/s41586-018-0509-0

Fang Bai 白芳

• Lab website: Link

CAS SIMM 中国科学院上海药物研究所

Mingyue Zheng 郑明月

• Lab website: Link

CAS CEMCS 中国科学院分子细胞科学卓越创新中心

Shaoqing Zhang 张少庆

• Lab website: Link
• Related Papers:
  • [JACS 2018] 设计含有金属离子簇的蛋白：https://pubs.acs.org/doi/10.1021/jacs.7b08261

Zhejiang University 浙江大学

Tingjun Hou 侯廷军

• Lab website: Link

Westlake University 西湖大学

Fajie Yuan 原发杰

• Lab website: Link
• Related Papers:
  • [ICLR 2024] SaProt: https://www.biorxiv.org/content/10.1101/2023.10.01.560349.abstract

Longxin Cao 曹龙兴

• Lab website: Link
• Related Papers:
  • [Nature 2022] RifGen/RifDock: https://www.nature.com/articles/s41586-022-04654-9, [Science 2020] SARS-CoV-2 minibinder design: https://www.science.org/doi/full/10.1126/science.abd9909

Zibo Chen 陈子博

• Lab website: Link
• Related Papers:
  • [Science 2020] Logic gate design: https://www.science.org/doi/full/10.1126/science.aay2790, [Nature 2019] Orthogonal protein heterodimers design: https://www.nature.com/articles/s41586-018-0802-y

Peilong Lu 卢培龙

• Lab website: Link
• Related Papers:
  • [Science 2018] Transmembrane protein design: https://www.science.org/doi/full/10.1126/science.aaq1739

Jianyang Zeng 曾坚阳

• Lab website: Link

Stan Z. Li 李子青

• Lab website: Link
• Related Papers:
  • [ICLR 2023] PiFold: https://arxiv.org/abs/2209.12643

Zhejiang University of Technology 浙江工业大学

Guijun Zhang 张贵军

• Lab website: Link

Sun Yat-sen University 中山大学

Yuedong Yang 杨跃东

• Lab website: Link

CAS SIAT 深圳先进技术研究院

Xiaozhou Luo 罗小舟

• Lab website: Link

Tsinghua SIGS 清华大学深圳国际研究生院

Feiran Li 李斐然

• Lab website: Link
• Related Papers: [
  • Nat Catalysis] DLKcat: https://www.nature.com/articles/s41929-022-00798-z

SUSTech 南方科技大学

Zhe Li 李喆

• Lab website: Link
• Related Papers:
  • [Nat Materials] 蛋白质晶体设计：https://www.nature.com/articles/s41563-023-01683-1

USTC 中国科学技术大学

Haiyan Liu 刘海燕

• Lab website: Link
• Related Papers:
  • [Nature Computational Science 2024] ABACUS-R: https://www.nature.com/articles/s43588-022-00273-6, [Nature 2022] SCUBA: https://www.nature.com/articles/s41586-021-04383-5

Qi Liu 刘淇

• Lab website: Link
• Related Papers:
  • [NeurIPS 2023] FAIR: https://arxiv.org/abs/2310.02553

Xiamen University 厦门大学

Xiaoping Min 闵小平

• Lab website: Link
• Related Papers:
  • PB-GPT

Shandong University 山东大学

Jianyi Yang 杨建益

• Lab website: Link

CAS TIB 中国科学院天津工业生物技术研究所

Huifeng Jiang 江会锋

• Lab website: Link
• Related Papers:
  • DeepEvo
  • Diffusion model for P450 generation