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David Baker

David Baker

Howard Hughes Medical Institute

ORCID: 0000-0001-7896-6217

Also affiliated with University of Washington

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 4%percentile

0.846Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Top data-sharing exemplar

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

Journal of Molecular Biology(2023)10.1016/j.jmb.2023.168021

Top 31%

0.630DataRank

Top 31%22 citations

Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin Webb, Augustin Žídek +20 more

Papers

Driven by 205 papers — median percentile 53. Top paper: “Protein Structure Prediction and Structural Genomics”.

Protein Structure Prediction and Structural Genomics

Science(2001)10.1126/science.1065659

N/A

18.9DataRank · unranked

1609 citations

Andrej Sali, David Baker

Mechanisms of protein folding

Current Opinion in Structural Biology(2001)10.1016/s0959-440x(00)00176-7

N/A

17.6DataRank · unranked

478 citations

Eric J Alm, David Baker, Arthur L Horwich, Viara Grantcharova

De novo design of luciferases using deep learning

Nature(2023)10.1038/s41586-023-05696-3

N/A

7.4DataRank · unranked

460 citations

Christoffer Norn, Yakov Kipnis, Doug Tischer, Samuel J. Pellock, Declan Evans +13 more

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

eLife(2020)10.7554/elife.57659

N/A

3.4DataRank · unranked

188 citations

Aleksandar Antanasijevic, Jorge A. Fallas, William Sheffler, Jeffrey Copps, Daniel Ellis +20 more

Local interactions and the optimization of protein folding

Proteins: Structure, Function, and Genetics(1997)10.1002/(sici)1097-0134(199711)29:3<282::aid-prot3>3.0.co;2-d

N/A

2.9DataRank · unranked

61 citations

Kim Simons, Hong Qian, David Baker, Ross Doyle

Characterization of the Substrate Specificity of a Human 5-Hydroxymethyluracil Glycosylase Activity

Chemical Research in Toxicology(2002)10.1021/tx010113b

N/A

2.7DataRank · unranked

40 citations

Pingfang Liu, Artur Burdzy, Lawrence C. Sowers, David Baker

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1914808117

N/A

2.1DataRank · unranked

63 citations

Danai Moschidi, Matthew J. Bick, Santrupti Nerli, Andrew C. McShan, Lauren Carter +6 more

De novo design of miniprotein antagonists of cytokine storm inducers

Nature Communications(2024)10.1038/s41467-024-50919-4

N/A

1.4DataRank · unranked

45 citations

Brian Coventry, Marta T. Borowska, Dimitrios C. Arhontoulis, Marc Expòsit, Mohamad H. Abedi +17 more

Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM

Nature Communications(2021)10.1038/s41467-021-25087-4

N/A

1.3DataRank · unranked

81 citations

Leigh M. Sewall, Christopher A. Cottrell, Diane G. Carnathan, Luis Jiménez, Julia T. Ngo +27 more

Accurate prediction of protein structures and interactions using a three-track neural network

Science(2021)10.1126/science.abj8754

N/A

1.3DataRank · unranked

5820 citations

Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee +27 more

Improved protein structure prediction using predicted interresidue orientations

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1914677117

N/A

1.1DataRank · unranked

1572 citations

Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker +1 more

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2314646121

N/A

1.1DataRank · unranked

44 citations

Natalie Brunette, Alex Goodson, Justas Dauparas, Sue Y. Yi, Erin C. Yang +9 more

De novo protein design by deep network hallucination

Nature(2021)10.1038/s41586-021-04184-w

N/A

0.964DataRank · unranked

617 citations

Samuel J. Pellock, Tamuka M. Chidyausiku, Theresa A. Ramelot, Sergey Ovchinnikov, Jingzhou Hao +10 more

Scaffolding protein functional sites using deep learning

Science(2022)10.1126/science.abn2100

N/A

0.926DataRank · unranked

478 citations

Sidney Lisanza, David Juergens, Doug Tischer, Joseph L. Watson, Karla M. Castro +19 more

Quadrivalent influenza nanoparticle vaccines induce broad protection

Nature(2021)10.1038/s41586-021-03365-x

N/A

0.868DataRank · unranked

325 citations

Daniel Ellis, Rebecca A. Gillespie, Geoffrey B. Hutchinson, Young‐Jun Park, Syed M. Moin +23 more

Designed proteins assemble antibodies into modular nanocages

Science(2021)10.1126/science.abd9994

N/A

0.785DataRank · unranked

186 citations

Ha V. Dang, George Ueda, Jorge A. Fallas, Ivan Vulovic, William Sheffler +25 more

Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry

Nature Protocols(2020)10.1038/s41596-019-0281-0

N/A

0.778DataRank · unranked

178 citations

Florian Büsch, Benjamin J. Jones, Mengxuan Jia, Zibo Chen, Scott E. Boyken +4 more

A Potent Anti-Malarial Human Monoclonal Antibody Targets Circumsporozoite Protein Minor Repeats and Neutralizes Sporozoites in the Liver

Immunity(2020)10.1016/j.immuni.2020.08.014

N/A

0.767DataRank · unranked

165 citations

Lais S. Pereira, Yevel Flores-García, James O’Connor, Barbara J. Flynn, Arne Schön +26 more

Next-Generation Surrogate Wnts Support Organoid Growth and Deconvolute Frizzled Pleiotropy In Vivo

Cell stem cell(2020)10.1016/j.stem.2020.07.020

N/A

0.757DataRank · unranked

154 citations

Andrew Ha, Wim de Lau, Kanako Yuki, António J. M. Santos, Changjiang You +28 more

Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules

UNC Libraries(2020)10.17615/8ga2-9t05

N/A

0.752DataRank · unranked

149 citations

Monica Berrondo, Andrew Leaver-Fay, James Thompson, S. I. Cooper, Daniel J. Mandell +27 more

Peptide-binding specificity prediction using fine-tuned protein structure prediction networks

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2216697120

N/A

0.722DataRank · unranked

122 citations

Justas Dauparas, Minkyung Baek, Mohamad H. Abedi, David Baker, Philip Bradley +1 more

Robust deep learning based protein sequence design using ProteinMPNN

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.03.494563

N/A

0.717DataRank · unranked

118 citations

Ivan Anishchenko, Nathaniel R. Bennett, Hua Bai, Robert J. Ragotte, Lukas F. Milles +17 more

Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle

Cell(2023)10.1016/j.cell.2023.08.017

N/A

0.705DataRank · unranked

109 citations

Larry A. Gallagher, Pia A. Andrade, Andi Liu, Ian R. Humphreys, Serdar Turkarslan +11 more

Design of multi-scale protein complexes by hierarchical building block fusion

Nature Communications(2021)10.1038/s41467-021-22276-z

N/A

0.678DataRank · unranked

91 citations

Rubul Mout, William Sheffler, Natasha I. Edman, Ivan Vulovic, Young‐Jun Park +15 more

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2012800118

N/A

0.657DataRank · unranked

79 citations

Sean D. Workman, Tianjun Sun, Stephen Rettie, Xinting Li, L.J. Worrall +12 more

Single-cell census of human tooth development enables generation of human enamel

Developmental Cell(2023)10.1016/j.devcel.2023.07.013

N/A

0.650DataRank · unranked

75 citations

Sesha Hanson-Drury, Anjali P. Patni, Devon Duron Ehnes, Yan Ting Zhao, Zicong Li +19 more

Targeting HIV Env immunogens to B cell follicles in nonhuman primates through immune complex or protein nanoparticle formulations

npj Vaccines(2020)10.1038/s41541-020-00223-1

N/A

0.641DataRank · unranked

71 citations

Christopher A. Cottrell, Aleksandar Antanasijevic, Diane G. Carnathan, Benjamin Cossette, Chiamaka A. Enemuo +19 more

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

Journal of Molecular Biology(2023)10.1016/j.jmb.2023.168021

Top 31%

0.630DataRank

Top 31%22 citations

Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin Webb, Augustin Žídek +20 more

Blueprinting extendable nanomaterials with standardized protein blocks

Nature(2024)10.1038/s41586-024-07188-4

N/A

0.624DataRank · unranked

63 citations

Yang Hsia, Ryan D. Kibler, Jinwei Xu, Neville P. Bethel, Deepesh Nagarajan +27 more

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2309457121

N/A

0.614DataRank · unranked

59 citations

Ross C. Bretherton, Justin Decarreau, Sangmin Lee, Nicole E. Gregorio, Natasha I. Edman +9 more

Accurate de novo design of high-affinity protein-binding macrocycles using deep learning

Nature Chemical Biology(2025)10.1038/s41589-025-01929-w

N/A

0.612DataRank · unranked

58 citations

David Juergens, Victor Adebomi, Yensi Flores Bueso, Qinqin Zhao, Alexandria N. Leveille +21 more

Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists

Science(2024)10.1126/science.adp1779

N/A

0.609DataRank · unranked

57 citations

Aditya Krishnakumar, Robert J. Ragotte, Inna Goreshnik, Brian Coventry, Asim K. Bera +10 more

Hierarchical design of pseudosymmetric protein nanocages

Nature(2024)10.1038/s41586-024-08360-6

N/A

0.564DataRank · unranked

42 citations

Young‐Jun Park, Chelsea N. Fries, Neil Gerstenmaier, Sebastian Ols, Erin C. Yang +10 more

Design of proteins presenting discontinuous functional sites using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.29.402743

N/A

0.553DataRank · unranked

39 citations

Sidney Lisanza, Jue Wang, Runze Dong, Ivan Anishchenko, Lukas F. Milles +3 more

Single Layers of Attention Suffice to Predict Protein Contacts

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.21.423882

N/A

0.538DataRank · unranked

35 citations

Neil Thomas, Roshan Rao, Justas Dauparas, Peter K. Koo, David Baker +3 more

Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants

Nature Biotechnology(2022)10.1038/s41587-022-01280-8

N/A

0.529DataRank · unranked

33 citations

Hsien‐Wei Yeh, Alexandra C. Walls, Basile I. M. Wicky, Kaitlin R. Sprouse, Laura A. VanBlargan +19 more

Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution

Nature Biotechnology(2024)10.1038/s41587-023-02107-w

N/A

0.529DataRank · unranked

33 citations

William H. Nguyen, Nathan Greenwood, John C. Rose, Shao‐En Ong, Dustin J. Maly +2 more

Protein sequence design by explicit energy landscape optimization

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.23.218917

N/A

0.520DataRank · unranked

31 citations

Basile I. M. Wicky, David Juergens, Sirui Liu, David E. Kim, Brian Koepnick +5 more

Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive antibody response against diverse coronavirus subgenera

Nature Communications(2023)10.1038/s41467-023-41661-4

N/A

0.515DataRank · unranked

30 citations

Olubukola M. Abiona, Cynthia T. Ziwawo, Anne P. Werner, Daniel Ellis, Yaroslav Tsybovsky +16 more

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Nature Communications(2021)10.1038/s41467-021-27222-7

N/A

0.500DataRank · unranked

27 citations

Sergey Lyskov, Steven M. Lewis, Jared Adolf‐Bryfogle, Rebecca F. Alford, Kyle A. Barlow +45 more

Isolating Conformers to Assess Dynamics of Peptidic Catalysts Using Computationally Designed Macrocyclic Peptides

ACS Catalysis(2021)10.1021/acscatal.1c01097

N/A

0.489DataRank · unranked

25 citations

Parisa Hosseinzadeh, Timothy W. Craven, Michael J. Robertson, Yaodong Han, Sheng‐Ying Hsieh +4 more

Computational design of soluble functional analogues of integral membrane proteins

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.09.540044

N/A

0.470DataRank · unranked

22 citations

Martin Pačesa, Nicolas Goldbach, L Dornfeld, Petra E. M. Balbi, Sandrine Georgeon +11 more

Design of pseudosymmetric protein hetero-oligomers

Nature Communications(2024)10.1038/s41467-024-54913-8

N/A

0.463DataRank · unranked

9 citations

Sangmin Lee, Madison Kennedy, Basile I. M. Wicky, Stella M. Lai, Marius M. Kostelic +9 more

Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function

Angewandte Chemie International Edition(2024)10.1002/anie.202414705

N/A

0.457DataRank · unranked

20 citations

Kiera H. Sumida, Jessica L. Caruso, David Baker, Jesse G. Zalatan, Brianne R. King

De novo design of protein homodimers containing tunable symmetric protein pockets

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2113400119

N/A

0.457DataRank · unranked

20 citations

Madison Kennedy, Kirsten A. Thompson, Michelle DeWitt, Brian Coventry, Alex Kang +6 more

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2214556120

N/A

0.442DataRank · unranked

18 citations

Alena Khmelinskaia, William Sheffler, Marcos C. Miranda, Aleksandar Antanasijevic, Andrew J. Borst +21 more

Multivalent designed proteins protect against SARS-CoV-2 variants of concern

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.07.451375

N/A

0.442DataRank · unranked

18 citations

James Brett Case, Young‐Jun Park, Longxing Cao, Kejia Wu, Alexandra C. Walls +41 more

Randomized gates eliminate bias in sort‐seq assays

Protein Science(2022)10.1002/pro.4401

N/A

0.416DataRank · unranked

15 citations

Buwei Huang, Erika A. DeBenedictis, Brian Coventry, Nicholas Bhattacharya, Kevin K. Yang +3 more

Hallucination of closed repeat proteins containing central pockets

Nature Structural & Molecular Biology(2023)10.1038/s41594-023-01112-6

N/A

0.396DataRank · unranked

13 citations

Derrick R. Hicks, Dmitri Zorine, Justas Dauparas, Basile I. M. Wicky, Lukas F. Milles +7 more

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2425459122

N/A

0.385DataRank · unranked

12 citations

Joseph L. Watson, David Juergens, Sagardip Majumder, Ria Sonigra, Stacey Gerben +5 more

De Novo Design of High-Performance Cortisol Luminescent Biosensors

Journal of the American Chemical Society(2025)10.1021/jacs.5c05004

N/A

0.378DataRank · unranked

10 citations

Peng Xue, Chenggang Xi, Gyu Rie Lee, David Baker, Hsien‐Wei Yeh +1 more

De novo design of Ras isoform selective binders

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.29.610300

N/A

0.360DataRank · unranked

10 citations

Xinting Li, Alexa Rane Batingana, Caixuan Liu, Hanlun Jiang, Kevin Shannon +4 more

Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.28.428677

N/A

0.345DataRank · unranked

9 citations

Leigh M. Sewall, Christopher A. Cottrell, Diane G. Carnathan, Luis Jiménez, Julia T. Ngo +27 more

Rapid and Sensitive Detection of Antigen from SARS-CoV-2 Variants of Concern by a Multivalent Minibinder-Functionalized Nanomechanical Sensor

Analytical Chemistry(2022)10.1021/acs.analchem.2c01221

N/A

0.345DataRank · unranked

9 citations

Andrew C. Hunt, Gajendra S. Shekhawat, Lauren Carter, Sidney Chan, Kejia Wu +9 more

Targeting HIV Env immunogens to B cell follicles in non-human primates through immune complex or protein nanoparticle formulations

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.19.956482

N/A

0.330DataRank · unranked

8 citations

Christopher A. Cottrell, Aleksandar Antanasijevic, Diane G. Carnathan, Benjamin Cossette, Chiamaka A. Enemuo +17 more

Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.27.221333

N/A

0.330DataRank · unranked

8 citations

Rubul Mout, William Sheffler, Natasha I. Edman, Ivan Vulovic, Young‐Jun Park +15 more

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.22.604663

N/A

0.330DataRank · unranked

8 citations

Joseph L. Watson, David Juergens, Sagardip Majumder, Ria Sonigra, Stacey Gerben +5 more

Accurate Computational Design of 3D Protein Crystals

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.18.517014

N/A

0.330DataRank · unranked

8 citations

Shunzhi Wang, Una Nattermann, Asim K. Bera, Andrew J. Borst, Matthew J. Bick +21 more

Hierarchical design of pseudosymmetric protein nanoparticles

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.16.545393

N/A

0.312DataRank · unranked

7 citations

Young‐Jun Park, Neil Gerstenmaier, Erin C. Yang, Adam J. Wargacki, Yang Hsia +8 more

Designed Endocytosis-Triggering Proteins mediate Targeted Degradation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.19.553321

N/A

0.312DataRank · unranked

7 citations

Mohamad H. Abedi, Green Ahn, Brian Coventry, Isaac Sappington, Rong Wang +38 more

Design of stimulus-responsive two-state hinge proteins

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.27.525968

N/A

0.312DataRank · unranked

7 citations

Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman +18 more

Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.03.668343

N/A

0.312DataRank · unranked

7 citations

Steffen Klein, Shajesh Sharma, David Juergens, Justin Decarreau, Bingxu Liu +14 more

Design of amyloidogenic peptide traps

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.13.523785

N/A

0.312DataRank · unranked

7 citations

Ewa Andrzejewska, Hannah L. Han, Enrico Rennella, Matthias M. Schneider, Georg Meisl +12 more

Solution mapping of MHC-I:TCR interactions using a minimalistic protein system

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2506016122

N/A

0.241DataRank · unranked

4 citations

Apala Chaudhuri, Xiaojing Chen, William L. White, K. Christopher García, David Baker +2 more

Hallucinating protein assemblies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.09.493773

N/A

0.241DataRank · unranked

4 citations

Lukas F. Milles, Alexis Courbet, Robert J. Ragotte, Justas Dauparas, Elias S. Kinfu +11 more

Intracellular delivery of proteins for live cell imaging

Journal of Controlled Release(2025)10.1016/j.jconrel.2025.113651

N/A

0.241DataRank · unranked

4 citations

Hwanhee C. Kim, Catherine Sniezek, S. A. Berger, Justin M. Kollman, David Baker +3 more

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.06.518550

Top 63%

0.216DataRank

Top 63%3 citations

Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin Webb, Augustin Žídek +20 more

Computational design of metalloproteases

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.20.689622

N/A

0.165DataRank · unranked

2 citations

Kejia Wu, Hojae Choi, Preetham Venkatesh, Samuel J. Pellock, Nikita Hanikel +13 more

Computational design of nanoscale rotational mechanics in de novo protein assemblies

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.11.468255

N/A

0.165DataRank · unranked

2 citations

Jesse M. Hansen, Yang Hsia, Neville P. Bethel, YJ. Park, Chunfu Xu +14 more

Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.02.560617

N/A

0.165DataRank · unranked

2 citations

Shao‐En Ong, David Baker, Dustin J. Maly, Jason Z. Zhang

The ΦPA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice

Research Square(2022)10.21203/rs.3.rs-1531074/v1

N/A

0.127DataRank · unranked

1 citations

Axel F. Brilot, Melissa Mèndez-Moran, Minkyung Baek, Junrui Li, Claire Kokontis +5 more

Computational stabilization of a non-heme iron enzyme enables efficient evolution of new function

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.18.590141

N/A

0.104DataRank · unranked

1 citations

Kiera H. Sumida, Jessica L. Caruso, David Baker, Jesse G. Zalatan, Brianne R. King

Computational design of potent and selective binders of BAK and BAX

Science Advances(2025)10.1126/sciadv.adt4170

N/A

0.104DataRank · unranked

1 citations

Erinna F. Lee, Tiffany J. Harris, Sharon Tran, Asim K. Bera, L. M. Miller +14 more

Hierarchical design of pseudosymmetric protein nanoparticles

Research Square(2023)10.21203/rs.3.rs-3074553/v1

N/A

0.104DataRank · unranked

1 citations

Quinton M. Dowling, Young‐Jun Park, Neil Gerstenmaier, Erin C. Yang, Adam J. Wargacki +8 more

A covariation analysis reveals elements of selectivity in quorum sensing systems

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.25.437039

N/A

0.104DataRank · unranked

1 citations

Qian Cong, Schaefer Al, EK MacLeod, Angelina Zimenko, David Baker +2 more

De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.12.544624

N/A

0DataRank · unranked

2 citations

Lei Shi, Ashley Chang, Xianchi Dong, Andres Fernandez, John C. Kraft +35 more

Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.02.539146

N/A

0DataRank · unranked

1 citations

Larry A. Gallagher, Pia A. Andrade, Andi Liu, Ian R. Humphreys, Serdar Turkarslan +11 more

De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs

Research Square(2023)10.21203/rs.3.rs-2736786/v1

N/A

0DataRank · unranked

0 citations

Shunzhi Wang, Madison Kennedy, Mariano Curti, George A. Sutherland, Cvetelin Vasilev +25 more

Corrigendum: Single cell RNA sequencing reveals human tooth type identity and guides in vitro hiPSC derived odontoblast differentiation (iOB)

Frontiers in Dental Medicine(2023)10.3389/fdmed.2023.1278809

N/A

0DataRank · unranked

0 citations

Anjali P. Patni, Deborah L. Lee, Ammar Alghadeer, Yan Ting Zhao, Devon Duron Ehnes +11 more

Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive antibody response against diverse coronavirus subgenera

UNC Libraries(2023)10.17615/cv2y-n773

N/A

0DataRank · unranked

0 citations

Charis Palandjian, Hutchinson G.B., C S, Ziwawo C.T., N. Wang +16 more

Improving Protein Expression, Stability, and Function with ProteinMPNN

Journal of the American Chemical Society(2024)10.1021/jacs.3c10941

N/A

0DataRank · unranked

314 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.21.600123

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bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.20.613980

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Nature(2025)10.1038/s41586-024-08393-x

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Science(2025)10.1126/science.adr8063

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Science(2025)10.1126/science.adv0185

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Cell chemical biology(2025)10.1016/j.chembiol.2025.01.006

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Molecular Cell(2025)10.1016/j.molcel.2025.09.020

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Journal of the American Chemical Society(2025)10.1021/jacs.5c02576

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8 citations

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Journal of Biomedical Materials Research Part A(2025)10.1002/jbm.a.37897

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11 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.14.648806

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.29.678898

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.12.681819

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.13.681693

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.30.696949

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.18.670751

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1 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.21.689808

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.16.664392

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Nature(2025)10.1038/s41586-025-09549-z

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Science(2020)10.1126/science.aba6527

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Science(2020)10.1126/science.abd9909

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Science(2020)10.1126/science.aay2790

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Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1908768117

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.30.125179

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.01.406611

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.16.385922

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.22.346965

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Science(2021)10.1126/science.abc8182

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Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2017228118

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Nature(2021)10.1038/s41586-020-03120-8

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Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2021569118

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eLife(2021)10.7554/elife.69169

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.10.468128

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.30.462231

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.12.435185

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.04.459002

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10 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.04.438423

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.22.449355

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4 citations

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Science(2022)10.1126/science.add2187

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Nature(2022)10.1038/s41586-022-04654-9

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Cell(2022)10.1016/j.cell.2022.07.019

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Science(2022)10.1126/science.abm1183

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Cell Reports(2022)10.1016/j.celrep.2022.110457

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Nature Machine Intelligence(2022)10.1038/s42256-021-00428-6

N/A

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31 citations

Alyssa La Fleur, Zibo Chen, Ajasja Ljubetič, David Baker, Sreeram Kannan +2 more

De novo design of obligate ABC-type heterotrimeric proteins

Nature Structural & Molecular Biology(2022)10.1038/s41594-022-00879-4

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30 citations

Andrew Favor, Ya‐Ting Chang, Andrew Norris, Scott E. Boyken, Yang Hsia +8 more

Isoform-specific inhibition of FGFR signaling achieved by a de-novo-designed mini-protein

Cell Reports(2022)10.1016/j.celrep.2022.111545

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11 citations

Jungyuen Choi, Longxing Cao, Jyotidarsini Mohanty, Yoshihisa Suzuki, Andy Park +4 more

Language models generalize beyond natural proteins

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.21.521521

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0DataRank · unranked

202 citations

Ori Kabeli, Yilun Du, Basile I. M. Wicky, Lukas F. Milles, Justas Dauparas +5 more

De novo design of high-affinity protein binders to bioactive helical peptides

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.10.519862

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22 citations

Philip J. Y. Leung, Isaac D. Lutz, Preetham Venkatesh, Joseph L. Watson, Fabian Hink +18 more

Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.01.494374

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10 citations

Jan Steinkühler, Timothy Q. Vu, Taylor F. Gunnels, Peilong Lu, David Baker +2 more

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.04.502842

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10 citations

Alena Khmelinskaia, William Sheffler, Marcos C. Miranda, Aleksandar Antanasijevic, Andrew J. Borst +21 more

The ϕPA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.06.487387

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0DataRank · unranked

7 citations

Axel F. Brilot, Melissa Mèndez-Moran, Minkyung Baek, Junrui Li, Claire Kokontis +5 more

Hallucination of closed repeat proteins containing central pockets

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.01.506251

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0DataRank · unranked

3 citations

Derrick R. Hicks, Dmitri Zorine, Justas Dauparas, Basile I. M. Wicky, Lukas F. Milles +7 more

De novo design of high-affinity binders of bioactive helical peptides

Nature(2023)10.1038/s41586-023-06953-1

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0DataRank · unranked

230 citations

Philip J. Y. Leung, Preetham Venkatesh, Isaac D. Lutz, Fabian Hink, Huu‐Hien Huynh +25 more

Design of stimulus-responsive two-state hinge proteins

Science(2023)10.1126/science.adg7731

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0DataRank · unranked

91 citations

Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman +18 more

Accurate computational design of three-dimensional protein crystals

Nature Materials(2023)10.1038/s41563-023-01683-1

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0DataRank · unranked

56 citations

Shunzhi Wang, Una Nattermann, Asim K. Bera, Andrew J. Borst, Muammer Y. Yaman +26 more

Time-tagged ticker tapes for intracellular recordings

Nature Biotechnology(2023)10.1038/s41587-022-01524-7

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0DataRank · unranked

55 citations

Xiuyuan Li, Eric M. Moult, Pojeong Park, Benjamin C. Tang, Hao Shen +7 more

De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8

Nature Communications(2023)10.1038/s41467-023-41272-z

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0DataRank · unranked

48 citations

Lei Shi, Ashley Chang, Xianchi Dong, Andres Fernandez, John C. Kraft +35 more

The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice

Nature Communications(2023)10.1038/s41467-023-36526-9

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0DataRank · unranked

41 citations

Axel F. Brilot, Melissa Mèndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li +5 more

Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds

Nature Chemical Biology(2023)10.1038/s41589-023-01313-6

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0DataRank · unranked

28 citations

Umut Y. Ulge, Alfredo Quijano‐Rubio, Zachary J. Bernstein, David R. Maestas, Jung-Ho Chun +20 more

De novo design of small beta barrel proteins

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2207974120

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36 citations

Davin R. Jensen, David Feldman, Doug Tischer, Ayesha Saleem, Cameron M. Chow +11 more

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

PLoS Computational Biology(2023)10.1371/journal.pcbi.1010680

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0DataRank · unranked

36 citations

Erin C. Yang, Quinton M. Dowling, Yang Hsia, Chelsea N. Fries, Jenna Stanislaw +9 more

Precisely patterned nanofibres made from extendable protein multiplexes

Nature Chemistry(2023)10.1038/s41557-023-01314-x

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0DataRank · unranked

29 citations

Andrew J. Borst, Fabio Parmeggiani, Matthew J. Bick, TJ Brunette, Hannah Nguyen +10 more

In vivo selection of synthetic nucleocapsids for tissue targeting

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2306129120

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0DataRank · unranked

8 citations

Halli Benasutti, Meilyn Sylvestre, Gabriel L. Butterfield, Gabriel J. Rocklin, Christian Richardson +14 more

De novo design of monomeric helical bundles for pH‐controlled membrane lysis

Protein Science(2023)10.1002/pro.4769

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0DataRank · unranked

10 citations

Issa Benna, Basile I. M. Wicky, Jacob T. Croft, Lauren Carter, Asim K. Bera +7 more

Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6

ACS Chemical Biology(2023)10.1021/acschembio.3c00113

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0DataRank · unranked

7 citations

Suchetana Gupta, Parisa Hosseinzadeh, Benjamin P. Brown, David Baker, David W. Christianson +1 more

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins

Biochemistry(2023)10.1021/acs.biochem.2c00497

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0DataRank · unranked

5 citations

Andrew J. Borst, Derrick R. Hicks, Isabelle Moczygemba, David Feldman, Brian Coventry +7 more

Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.09.561603

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110 citations

Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet +14 more

Small-molecule binding and sensing with a designed protein family

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.01.565201

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34 citations

Samuel J. Pellock, Christoffer Norn, Doug Tischer, Justas Dauparas, Ivan Anischenko +14 more

Computational design of sequence-specific DNA-binding proteins

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.20.558720

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28 citations

Robert Pecoraro, Ryan McHugh, Lindsey Doyle, Wei Chen, Olivier Boivin +15 more

De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.20.572602

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14 citations

Meerit Y. Said, Long Tran, Sagardip Majumder, Inna Goreshnik, Gyu Rie Lee +20 more

Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.14.532666

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10 citations

Rachel L. Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay Srivatsan, Ali Etemadi +27 more

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.04.551935

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0DataRank · unranked

10 citations

Natalie Brunette, Alexander M.C. Goodson, Justas Dauparas, Sue Yi, Erin C. Yang +9 more

Stepwise design of pseudosymmetric protein hetero-oligomers

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.07.535760

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7 citations

Sangmin Lee, Madison Kennedy, Basile I. M. Wicky, Stella M. Lai, Marius M. Kostelic +7 more

Massively parallel protein-protein interaction measurement by sequencing (MP3-seq) enables rapid screening of protein heterodimers

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.08.527770

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6 citations

Alyssa La Fleur, Benjamin Groves, Cirstyn Michel, David Baker, Ajasja Ljubetič +2 more

Blueprinting expandable nanomaterials with standardized protein building blocks

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.09.544258

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6 citations

Yang Hsia, Ryan D. Kibler, Jinwei Xu, Neville P. Bethel, Deepesh Nagarajan +26 more

Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.16.545341

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0DataRank · unranked

5 citations

Ryan D. Kibler, Yang Hsia, Andrew J. Borst, Annika Philomin, Madison Kennedy +3 more

De novo designed Hsp70 activator dissolves intracellular condensates

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.18.558356

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3 citations

Nathan Greenwood, Jason Hernandez, Josh T. Cuperus, Buwei Huang, Bryan D. Ryder +4 more