ReviewNature methods2020
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Abstract readReview
In one paragraph
Review in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 512 papers.
0numbers the graph read from it
0cells of the map it votes in
512citing papers in PubMed
–field-weighted citation impact
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.
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.
Who cites it
512 citing papers in PubMed.
- Investigating the effects of missense mutations on the dual Ras/Rap activation mechanism of SYNGAP1 using molecular modelling.Journal of structural biology: X · 2026Article
- Validation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition.Molecular systems biology · 2026Article
- KU80 suppresses endonuclease G activity to preserve genomic integrity.The FEBS journal · 2026Article
- Solid-state nanopore sensing: the next workhorse of biophysical characterization.Nature methods · 2026Review
- Bioinspired peptide cyclisation enables exploration of cytochrome P450 catalysed sequential oxidation in rufomycin biosynthesis.Chemical science · 2026Article
- De novo design of semisynthetic conduction pores.Nature structural & molecular biology · 2026Article
- Reimagining computational macromolecular modeling: AI-driven approaches.Biophysical journal · 2026Review
- IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.Journal of molecular biology · 2026Article
- Fast activity prediction of chemically modified siRNAs via structure-based energy calculations and inference-augmented tabular deep learning.Molecular therapy. Nucleic acids · 2026Article
- High-throughput ligand diversification to discover chemical inducers of proximity.Nature chemical biology · 2026Article
- Upcycling Vegetable Waste Into Functional Food Ingredients via Synergistic Microbial Engineering and Artificial Intelligence.Comprehensive reviews in food science and food safety · 2026Review
- Accelerating protein design by scaling experimental characterization.Nature communications · 2026Article
- Improved Stability and Brightness Following Iterative Redesign of a De Novo Biliprotein.Biochemistry · 2026Article
- Structure-based TCR-pMHC binding prediction and generalization to unseen peptides.npj drug discovery · 2026Article
- Crystal structures of type T archaeal ribonuclease P Rpp30, Rpp30/Pop5, and L7Ae provide insights into a reduced RNase P.Nucleic acids research · 2026Article
- Structure-Guided Extremophile Genome Mining Expands the PETase Landscape and Reveals PET-Hydrolysing True Lipase Lineages.Microbial biotechnology · 2026Article
- Article
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide.Journal of chemical information and modeling · 2026Article
- Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion.bioRxiv : the preprint server for biology · 2026Article
452 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
108 authors.
Julia Koehler Leman *Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.ORCID http://orcid.org/0000-0002-5693-3593
Brian D Weitzner *Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Steven M Lewis *Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Jared Adolf-BryfogleDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Nawsad AlamDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Rebecca F AlfordDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Melanie AprahamianDepartment of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
David BakerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0001-7896-6217
Kyle A BarlowGraduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-9787-0066
Patrick BarthInstitute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
Benjamin BasantaDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-1118-5269
Brian J BenderDepartment of Pharmacology, Vanderbilt University, Nashville, TN, USA.
Kristin BlacklockInstitute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Jaume BonetInstitute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.ORCID http://orcid.org/0000-0001-5210-4387
Scott E BoykenInstitute for Protein Design, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-5378-0632
Phil BradleyFred Hutchinson Cancer Research Center, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-0224-6464
Chris BystroffDepartment of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
Patrick ConwayDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Seth CooperKhoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
Bruno E CorreiaInstitute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.ORCID http://orcid.org/0000-0002-7377-8636
Brian CoventryDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Rhiju DasDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-7497-0972
René M De JongDSM Biotechnology Center, Delft, the Netherlands.
Frank DiMaioDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Lorna DsilvaKhoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
Roland DunbrackInstitute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0001-7674-6667
Alexander S FordDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Brandon FrenzInstitute for Protein Design, University of Washington, Seattle, WA, USA.
Darwin Y FuDepartment of Chemistry, Vanderbilt University, Nashville, TN, USA.
Caleb GeniesseDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-7897-8338
Lukasz GoldschmidtDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Ragul GowthamanUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.ORCID http://orcid.org/0000-0002-0008-6401
Jeffrey J GrayDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-6380-2324
Dominik GrontFaculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
Sharon GuffyDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Scott HorowitzDepartment of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.
Po-Ssu HuangDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Thomas HuberResearch School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
Tim M JacobsProgram in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Jeliazko R JeliazkovProgram in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
David K JohnsonCenter for Computational Biology, University of Kansas, Lawrence, KS, USA.ORCID http://orcid.org/0000-0003-4262-8173
Kalli KappelBiophysics Program, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-2129-199X
John KaranicolasInstitute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-0300-726X
Hamed KhakzadSwiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID http://orcid.org/0000-0002-8556-0650
Karen R KharCyrus Biotechnology, Seattle, WA, USA.
Sagar D KhareInstitute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Firas KhatibDepartment of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.ORCID http://orcid.org/0000-0002-6817-7297
Alisa KhramushinDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Indigo C KingDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Robert KleffnerKhoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
Brian KoepnickDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Tanja KortemmeDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-8494-680X
Georg KuenzeDepartment of Chemistry, Vanderbilt University, Nashville, TN, USA.
Brian KuhlmanDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID http://orcid.org/0000-0003-4907-9699
Daisuke KurodaMedical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0003-2390-4785
Jason W LabonteDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Jason K LaiBaylor College of Medicine, Department of Pharmacology, Houston, TX, USA.
Gideon LapidothDepartment of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
Andrew Leaver-FayDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Steffen LindertDepartment of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
Thomas LinskyDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Nir LondonDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Joseph H LubinDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Sergey LyskovDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Jack MaguireProgram in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Lars MalmströmSwiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID http://orcid.org/0000-0001-9885-9312
Enrique MarcosDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0001-8736-4082
Orly MarcuDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Nicholas A MarzeDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Jens MeilerCenter for Structural Biology, Vanderbilt University, Nashville, TN, USA.
Rocco MorettiDepartment of Chemistry, Vanderbilt University, Nashville, TN, USA.
Vikram Khipple MulliganCenter for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
Santrupti NerliDepartment of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA.
Christoffer NornDepartment of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
Shane Ó'ConchúirDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Noah OllikainenDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Sergey OvchinnikovDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Michael S PacellaDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Xingjie PanDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Hahnbeom ParkDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Ryan E PavloviczDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Manasi PetheDepartment of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.
Brian G PierceUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.ORCID http://orcid.org/0000-0003-4821-0368
Kala Bharath PillaResearch School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
Barak RavehDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
P Douglas RenfrewCenter for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
Shourya S Roy BurmanDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-9274-9104
Aliza RubensteinInstitute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Marion F SauerChemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.
Andreas ScheckInstitute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
William SchiefDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-1120-0150
Ora Schueler-FurmanDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Yuval SedanDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Alexander M SevyChemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.ORCID http://orcid.org/0000-0002-2380-2861
Nikolaos G SgourakisDepartment of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
Lei ShiDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Justin B SiegelDepartment of Chemistry, University of California, Davis, Davis, CA, USA.
Daniel-Adriano SilvaDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Shannon SmithDepartment of Chemistry, Vanderbilt University, Nashville, TN, USA.
Yifan SongDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Amelie SteinDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-5862-1681
Maria SzegedyDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.ORCID http://orcid.org/0000-0003-2460-0900
Frank D TeetsDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Summer B ThymeDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Ray Yu-Ruei WangDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Andrew WatkinsDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Lior ZimmermanDepartment of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Richard BonneauCenter for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.ORCID http://orcid.org/0000-0003-4354-7906
Funding
WORD PROCESSING CENTER--COREP30CA006927 · NCI · RESEARCH INST OF FOX CHASE CAN CTR · PI Dietmar J Kappes · 1985 to 2026
$138.8MWorkshop on Environmental Technology Transfer and EntrepreneurshipP42ES004699 · NIEHS · UNIVERSITY OF CALIFORNIA DAVIS · PI HAMMOCK, BRUCE D · 1987 to 2021
$50.1MX-RAY STRUCTURE OF RIFM PROTEIN FROM THE BIOSYNTHESIS PATHWAY OF THE ANSAMYCIN AP41RR012408 · NCRR · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI MARIUZZA, ROY A · 1998 to 2011
$32.2MDecrypting Variants of Uncertain Significance in Long-QT SyndromeR01HL122010 · NHLBI · VANDERBILT UNIVERSITY · PI GEORGE, ALFRED L., SANDERS, CHARLES R · 2014 to 2025
$15.5MStructure based design of antibodies and vaccinesU19AI117905 · NIAID · VANDERBILT UNIVERSITY MEDICAL CENTER · PI SCHIEF, WILLIAM R. · 2015 to 2019
$12.0MTRAINING IN PHARMACOLOGICAL SCIENCEST32GM007628 · NIGMS · VANDERBILT UNIVERSITY · PI BARNETT, JOEY VICTOR, KAVALALI, EGE T · 1985 to 2022
$11.2MPATHOGENESIS AND IMMUNOLOGY OF DISEASET32AI007244 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI NEMAZEE, DAVID · 1985 to 2022
$8.8MTRAINING IN MOLECULAR BIOPHYSICST32GM008268 · NIGMS · UNIVERSITY OF WASHINGTON · PI KOLLMAN, JUSTIN M, ZHENG, NING · 1988 to 2023
$8.6MROSETTA An Integrated Protein Structure Modeling SuiteR01GM073151 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI KUHLMAN, BRIAN A · 2005 to 2019
$7.8MNext-generation computational/chemical methods for complex RNA structuresR35GM122579 · NIGMS · STANFORD UNIVERSITY · PI Rhiju Das · 2017 to 2026
$7.2MStructural Bioinformatics of Proteins and Protein Complexes and Applications to Cancer BiologyR35GM122517 · NIGMS · RESEARCH INST OF FOX CHASE CAN CTR · PI ROLAND L DUNBRACK · 2017 to 2026
$6.3MGPU workstation for deep learning-based protein design and cryo-EM data processingR35GM131923 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI BRIAN A KUHLMAN · 2019 to 2026
$6.1MAmerican Heart Association-American Stroke Association 18POST34080422Howard Hughes Medical InstituteNCI NIH HHS F31 CA243353NCI NIH HHS F32 CA189246NCI NIH HHS P30 CA006927NCI NIH HHS R21 CA219847NCI NIH HHS RL1 CA133832NCI NIH HHS UH2 CA203780NCRR NIH HHS P41 RR012408NHLBI NIH HHS R01 HL122010NIAID NIH HHS R01 AI113867NIAID NIH HHS R01 AI143997NIAID NIH HHS R21 AI121799NIAID NIH HHS T32 AI007244NIAID NIH HHS U19 AI117905NIDDK NIH HHS R01 DK097376NIEHS NIH HHS P42 ES004699NIEHS NIH HHS R35 ES030443NIGMS NIH HHS F31 GM123616NIGMS NIH HHS F32 GM110899NIGMS NIH HHS R00 GM120388NIGMS NIH HHS R01 GM073151NIGMS NIH HHS R01 GM073960NIGMS NIH HHS R01 GM076324NIGMS NIH HHS R01 GM078221NIGMS NIH HHS R01 GM080403NIGMS NIH HHS R01 GM084453NIGMS NIH HHS R01 GM088277NIGMS NIH HHS R01 GM092802NIGMS NIH HHS R01 GM097207NIGMS NIH HHS R01 GM098101NIGMS NIH HHS R01 GM099827NIGMS NIH HHS R01 GM099842NIGMS NIH HHS R01 GM099959NIGMS NIH HHS R01 GM110089NIGMS NIH HHS R01 GM117189NIGMS NIH HHS R01 GM117968NIGMS NIH HHS R01 GM121487NIGMS NIH HHS R01 GM123089NIGMS NIH HHS R01 GM126299NIGMS NIH HHS R01 GM127578NIGMS NIH HHS R01 GM132565NIGMS NIH HHS R21 GM102716NIGMS NIH HHS R35 GM122517NIGMS NIH HHS R35 GM122579NIGMS NIH HHS R35 GM125034NIGMS NIH HHS R35 GM131923NIGMS NIH HHS T32 GM007628NIGMS NIH HHS T32 GM008268NIGMS NIH HHS T32 GM135141
Abstract
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.
Indexed as
Models, MolecularSoftwareMacromolecular SubstancesMolecular Docking SimulationPeptidomimeticsProtein ConformationProteinsMacromolecular SubstancesPeptidomimeticsProteins
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
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.