Macromolecular modeling and design in Rosetta: recent methods and frameworks

Julia Koehler Leman^#^{1

2}, Brian D Weitzner^#^{3

4

5

6}, Steven M Lewis^#^{7

8

9}, Jared Adolf-Bryfogle¹⁰, Nawsad Alam¹¹, Rebecca F Alford³, Melanie Aprahamian¹², David Baker^{4

5}, Kyle A Barlow¹³, Patrick Barth^{14

15}, Benjamin Basanta^{4

16}, Brian J Bender¹⁷, Kristin Blacklock¹⁸, Jaume Bonet^{14

19}, Scott E Boyken^{5

6}, Phil Bradley²⁰, Chris Bystroff²¹, Patrick Conway⁴, Seth Cooper²², Bruno E Correia^{14

19}, Brian Coventry⁴, Rhiju Das²³, René M De Jong²⁴, Frank DiMaio^{4

5}, Lorna Dsilva²², Roland Dunbrack²⁵, Alexander S Ford⁴, Brandon Frenz^{5

9}, Darwin Y Fu²⁶, Caleb Geniesse²³, Lukasz Goldschmidt⁴, Ragul Gowthaman^{27

28}, Jeffrey J Gray^{3

29}, Dominik Gront³⁰, Sharon Guffy⁷, Scott Horowitz^{31

32}, Po-Ssu Huang⁴, Thomas Huber³³, Tim M Jacobs³⁴, Jeliazko R Jeliazkov²⁹, David K Johnson³⁵, Kalli Kappel³⁶, John Karanicolas²⁵, Hamed Khakzad^{19

37

38}, Karen R Khar^{9

35}, Sagar D Khare^{18

39

40

41

42}, Firas Khatib⁴³, Alisa Khramushin¹¹, Indigo C King^{4

9}, Robert Kleffner²², Brian Koepnick⁴, Tanja Kortemme⁴⁴, Georg Kuenze^{26

45}, Brian Kuhlman⁷, Daisuke Kuroda^{46

47}, Jason W Labonte^{3

48}, Jason K Lai¹⁵, Gideon Lapidoth⁴⁹, Andrew Leaver-Fay⁷, Steffen Lindert¹², Thomas Linsky^{4

5}, Nir London¹¹, Joseph H Lubin³, Sergey Lyskov³, Jack Maguire³⁴, Lars Malmström^{19

37

38

50}, Enrique Marcos^{4

51}, Orly Marcu¹¹, Nicholas A Marze³, Jens Meiler^{45

52

53}, Rocco Moretti²⁶, Vikram Khipple Mulligan^{54

4

5}, Santrupti Nerli⁵⁵, Christoffer Norn⁴⁹, Shane Ó'Conchúir⁴⁴, Noah Ollikainen⁴⁴, Sergey Ovchinnikov^{4

5

56}, Michael S Pacella³, Xingjie Pan⁴⁴, Hahnbeom Park⁴, Ryan E Pavlovicz^{4

5

9}, Manasi Pethe^{40

41}, Brian G Pierce^{27

28}, Kala Bharath Pilla³³, Barak Raveh¹¹, P Douglas Renfrew⁵⁴, Shourya S Roy Burman³, Aliza Rubenstein^{18

42}, Marion F Sauer⁵⁷, Andreas Scheck^{14

19}, William Schief¹⁰, Ora Schueler-Furman¹¹, Yuval Sedan¹¹, Alexander M Sevy⁵⁷, Nikolaos G Sgourakis⁵⁸, Lei Shi^{4

5}, Justin B Siegel^{59

60

61}, Daniel-Adriano Silva⁴, Shannon Smith²⁶, Yifan Song^{4

5

9}, Amelie Stein⁴⁴, Maria Szegedy³⁹, Frank D Teets⁷, Summer B Thyme⁴, Ray Yu-Ruei Wang⁴, Andrew Watkins²³, Lior Zimmerman¹¹, Richard Bonneau^{62

63

64

65}

Affiliations

¹ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.
² Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu.
³ Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁴ Department of Biochemistry, University of Washington, Seattle, WA, USA.
⁵ Institute for Protein Design, University of Washington, Seattle, WA, USA.
⁶ Lyell Immunopharma Inc., Seattle, WA, USA.
⁷ Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁸ Department of Biochemistry, Duke University, Durham, NC, USA.
⁹ Cyrus Biotechnology, Seattle, WA, USA.
¹⁰ Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
¹¹ Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
¹² Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
¹³ Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA.
¹⁴ Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
¹⁵ Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.
¹⁶ Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA.
¹⁷ Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
¹⁸ Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
¹⁹ Swiss Institute of Bioinformatics, Lausanne, Switzerland.
²⁰ Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
²¹ Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
²² Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
²³ Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
²⁴ DSM Biotechnology Center, Delft, the Netherlands.
²⁵ Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.
²⁶ Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
²⁷ University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
²⁸ Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
²⁹ Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
³⁰ Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
³¹ Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.
³² The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.
³³ Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
³⁴ Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
³⁵ Center for Computational Biology, University of Kansas, Lawrence, KS, USA.
³⁶ Biophysics Program, Stanford University, Stanford, CA, USA.
³⁷ Institute for Computational Science, University of Zurich, Zurich, Switzerland.
³⁸ S3IT, University of Zurich, Zurich, Switzerland.
³⁹ Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁴⁰ Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.
⁴¹ Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁴² Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁴³ Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.
⁴⁴ Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
⁴⁵ Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
⁴⁶ Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.
⁴⁷ Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan.
⁴⁸ Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA.
⁴⁹ Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
⁵⁰ Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.
⁵¹ Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
⁵² Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.
⁵³ Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA.
⁵⁴ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
⁵⁵ Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA.
⁵⁶ Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
⁵⁷ Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.
⁵⁸ Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
⁵⁹ Department of Chemistry, University of California, Davis, Davis, CA, USA.
⁶⁰ Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.
⁶¹ Genome Center, University of California, Davis, Davis, CA, USA.
⁶² Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.
⁶³ Department of Biology, New York University, New York, New York, USA. Bonneau@nyu.edu.
⁶⁴ Department of Computer Science, New York University, New York, NY, USA. Bonneau@nyu.edu.
⁶⁵ Center for Data Science, New York University, New York, NY, USA. Bonneau@nyu.edu.

^# Contributed equally.

PMID: 32483333
PMCID: PMC7603796
DOI: 10.1038/s41592-020-0848-2

Review

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Julia Koehler Leman et al. Nat Methods. 2020 Jul.

. 2020 Jul;17(7):665-680.

doi: 10.1038/s41592-020-0848-2. Epub 2020 Jun 1.

Authors

Affiliations

¹ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.
² Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu.
³ Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁴ Department of Biochemistry, University of Washington, Seattle, WA, USA.
⁵ Institute for Protein Design, University of Washington, Seattle, WA, USA.
⁶ Lyell Immunopharma Inc., Seattle, WA, USA.
⁷ Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁸ Department of Biochemistry, Duke University, Durham, NC, USA.
⁹ Cyrus Biotechnology, Seattle, WA, USA.
¹⁰ Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
¹¹ Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
¹² Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
¹³ Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA.
¹⁴ Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
¹⁵ Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.
¹⁶ Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA.
¹⁷ Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
¹⁸ Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
¹⁹ Swiss Institute of Bioinformatics, Lausanne, Switzerland.
²⁰ Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
²¹ Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
²² Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
²³ Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
²⁴ DSM Biotechnology Center, Delft, the Netherlands.
²⁵ Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.
²⁶ Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
²⁷ University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
²⁸ Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
²⁹ Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
³⁰ Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
³¹ Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.
³² The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.
³³ Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
³⁴ Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
³⁵ Center for Computational Biology, University of Kansas, Lawrence, KS, USA.
³⁶ Biophysics Program, Stanford University, Stanford, CA, USA.
³⁷ Institute for Computational Science, University of Zurich, Zurich, Switzerland.
³⁸ S3IT, University of Zurich, Zurich, Switzerland.
³⁹ Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁴⁰ Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.
⁴¹ Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁴² Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁴³ Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.
⁴⁴ Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
⁴⁵ Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
⁴⁶ Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.
⁴⁷ Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan.
⁴⁸ Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA.
⁴⁹ Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
⁵⁰ Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.
⁵¹ Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
⁵² Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.
⁵³ Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA.
⁵⁴ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
⁵⁵ Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA.
⁵⁶ Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
⁵⁷ Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.
⁵⁸ Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
⁵⁹ Department of Chemistry, University of California, Davis, Davis, CA, USA.
⁶⁰ Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.
⁶¹ Genome Center, University of California, Davis, Davis, CA, USA.
⁶² Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.
⁶³ Department of Biology, New York University, New York, New York, USA. Bonneau@nyu.edu.
⁶⁴ Department of Computer Science, New York University, New York, NY, USA. Bonneau@nyu.edu.
⁶⁵ Center for Data Science, New York University, New York, NY, USA. Bonneau@nyu.edu.

^# Contributed equally.

PMID: 32483333
PMCID: PMC7603796
DOI: 10.1038/s41592-020-0848-2

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.

PubMed Disclaimer

Figures

**Figure 1:. Capabilities of the Rosetta macromolecular modeling suite**
Some popular tasks that can be addressed in Rosetta (blue) and major systems that can be modeled (red). Note this is an incomplete list of Rosetta’s broad modeling capabilities.

**Figure 2:. Main elements of Rosetta are scoring and sampling**
(A) Three main elements are required in a Rosetta protocol. The *Pose* is the biomolecule, such as a protein, RNA, DNA, small molecule, or glycan, in a specific conformation. Residues in the *Pose* can be selected via *ResidueSelectors* and the behavior for side-chain optimization or mutation can be defined by *TaskOperations*. Specific *Movers* then control how the conformation of the *Pose* is changed, and the new conformation is subsequently evaluated by a *ScoreFunction*. The Metropolis criterion decides whether the new conformation is accepted during sampling. Many independent sampling trajectories are generated, and the final models are evaluated based on the purpose of the protocol. (B) The score function consists of a weighted linear combination of various score terms, highlighted in the figure and described above.

**Figure 3:. Rosetta can successfully address diverse biological questions**
(A) Curved β-sheet design: overlay of the designed homo-dimeric curved β-sheet (dcs-E_4_dim_cav3) in rainbow and the crystal structure in gray (PDBID 5u35). The protein is designed *de novo* and features a curved β-sheet, a large pocket, and a homodimer interface. (B) Parametric design: overlay of the *de novo* designed macrocycle 3H1 in blue and the NMR structure in gray (PDBID 5v2g). This “CovCore” (covalent core) miniprotein is held together covalently by a hydrophobic cross-linker at its core (in red for the design and gray for the NMR structure). (C) PyTXMS: the interactome of M1 protein (virulence factor of Group A *streptococcus*) and 15 human plasma proteins on the surface of bacteria (peptidoglycan layer (dark green), and the membrane (brown)). This 1.8MDa structure contains over 200 chemical cross-links and is measured in a complex mixture of intact bacteria and human plasma. All models are provided by Rosetta: M1 protein (gray), IgG (red), four fibrinogens (dark to light blue), six albumins (dark to light pink), coagulation factor XIII A [F13A] (purple), C4bPa (cyan), haptoglobin [HP] (brown), and alpha-1-antitrypsin [SerpinA1] (plum). (D) RosettaSurface: model of an LK-α peptide (LKKLLKLLKKLLKL with a periodicity of 3.5 assuming a helical conformation) on a hydrophilic self-assembled monolayer surface. The peptide is unstructured in solution and assumes helical structure when on the surface, as experiments show. (E) RosettaCarbohydrate: flexible docking of a carbohydrate antigen to an antibody. The crystal structure is in gray (PDBID 1mfa) and the model in blue, with the carbohydrate in green. Antibody coordinates were taken from the PDB and glycan coordinates started from a randomized backbone conformation and rigid-body orientation. (F) PIPER-FlexPepDock: high-resolution model of a peptide-protein complex (model: blue; solved structure in gray, PDBID 1mfg). The model was generated from a peptide sequence (LDVPV, derived from the C-terminal tail of ErbB2R) and the unbound structure of the receptor (Erbin PDZ domain, PDBID 2h3l, colored in red).

**Figure 4:. User interfaces to the codebase**
(A) Rosetta can be run from a terminal and offers three interfaces to the codebase. The top panel outlines the task to be accomplished: making two mutations in a protein and then refining the structure. The panels underneath show how this task can be accomplished in the different interfaces. The command line panel shows the executable, input files and options to run two specific applications. RosettaScripts is an XML-based scripting language that offers more flexibility by combining *Movers* and *ScoreFunctions* into a custom *Protocol*. PyRosetta offers direct access to the underlying code objects but requires knowledge of the codebase. (B) Point-and-click interfaces to the codebase. InteractiveRosetta is a graphical user-interface (GUI) to PyRosetta. It offers controls to the most popular protocols, file formats and options. Foldit is a videogame primarily used to crowd-source real-world scientific puzzles but can also be used on custom proteins of interest. It can run some popular applications via a game interface. ROSIE hosts a multitude of servers each executing a particular protocol. It currently includes servers for 21 Rosetta methods. [The InteractiveRosetta and Foldit panels were originally published in and under Creative Commons licenses that allows reproduction as is.]

**Figure 5:. Main external documentation page**
In 2015, our community performed a complete overhaul of our documentation. Documentation is now hosted on a Gollum wiki, which is version controlled and easily editable by members of our community. Accessibility and ability to edit the documentation has drastically improved the user-experience of the software.

See this image and copyright information in PMC

References

1. Schrodinger - Biologics Design. at <https://www.schrodinger.com/science-articles/biologics-design>
1. Molecular Operating Environment (MOE) | MOEsaic | PSILO. at <https://www.chemcomp.com/Products.htm>
1. Ref. Dassault Systèmes BIOVIA, Discovery Studio Modeling Environment, Release 2017, San Diego: Dassault Systèmes, 2016. at <https://www.3dsbiovia.com/products/collaborative-science/biovia-discover...>
1. Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ & Söding J HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019). - PMC - PubMed
1. Vu O, Mendenhall J, Altarawy D & Meiler J BCL::Mol2D—a robust atom environment descriptor for QSAR modeling and lead optimization. J. Comput. Aided. Mol. Des. 33, 477–486 (2019). - PMC - PubMed

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Macromolecular modeling and design in Rosetta: recent methods and frameworks

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Macromolecular modeling and design in Rosetta: recent methods and frameworks

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