Nature Communications (Nov 2021)
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
- Julia Koehler Leman,
- Sergey Lyskov,
- Steven M. Lewis,
- Jared Adolf-Bryfogle,
- Rebecca F. Alford,
- Kyle Barlow,
- Ziv Ben-Aharon,
- Daniel Farrell,
- Jason Fell,
- William A. Hansen,
- Ameya Harmalkar,
- Jeliazko Jeliazkov,
- Georg Kuenze,
- Justyna D. Krys,
- Ajasja Ljubetič,
- Amanda L. Loshbaugh,
- Jack Maguire,
- Rocco Moretti,
- Vikram Khipple Mulligan,
- Morgan L. Nance,
- Phuong T. Nguyen,
- Shane Ó Conchúir,
- Shourya S. Roy Burman,
- Rituparna Samanta,
- Shannon T. Smith,
- Frank Teets,
- Johanna K. S. Tiemann,
- Andrew Watkins,
- Hope Woods,
- Brahm J. Yachnin,
- Christopher D. Bahl,
- Chris Bailey-Kellogg,
- David Baker,
- Rhiju Das,
- Frank DiMaio,
- Sagar D. Khare,
- Tanja Kortemme,
- Jason W. Labonte,
- Kresten Lindorff-Larsen,
- Jens Meiler,
- William Schief,
- Ora Schueler-Furman,
- Justin B. Siegel,
- Amelie Stein,
- Vladimir Yarov-Yarovoy,
- Brian Kuhlman,
- Andrew Leaver-Fay,
- Dominik Gront,
- Jeffrey J. Gray,
- Richard Bonneau
Affiliations
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation
- Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
- Steven M. Lewis
- Cyrus Biotechnology
- Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, Scripps Research
- Rebecca F. Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
- Kyle Barlow
- Graduate Program in Bioinformatics, University of California San Francisco
- Ziv Ben-Aharon
- Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School
- Daniel Farrell
- Department of Biochemistry, University of Washington
- Jason Fell
- Genome Center, University of California
- William A. Hansen
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey
- Ameya Harmalkar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
- Jeliazko Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University
- Georg Kuenze
- Department of Chemistry, Vanderbilt University
- Justyna D. Krys
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1
- Ajasja Ljubetič
- Department of Biochemistry, University of Washington
- Amanda L. Loshbaugh
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco
- Jack Maguire
- Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill
- Rocco Moretti
- Department of Chemistry, Vanderbilt University
- Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, Simons Foundation
- Morgan L. Nance
- Program in Molecular Biophysics, Johns Hopkins University
- Phuong T. Nguyen
- Department of Physiology and Membrane Biology, School of Medicine, University of California
- Shane Ó Conchúir
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco
- Shourya S. Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
- Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
- Shannon T. Smith
- Center for Structural Biology, Vanderbilt University
- Frank Teets
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill
- Johanna K. S. Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen
- Andrew Watkins
- Department of Biochemistry, Stanford University School of Medicine
- Hope Woods
- Center for Structural Biology, Vanderbilt University
- Brahm J. Yachnin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey
- Christopher D. Bahl
- Institute for Protein Innovation
- Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth
- David Baker
- Department of Biochemistry, University of Washington
- Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine
- Frank DiMaio
- Department of Biochemistry, University of Washington
- Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey
- Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco
- Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
- Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen
- Jens Meiler
- Department of Chemistry, Vanderbilt University
- William Schief
- Department of Immunology and Microbiology, Scripps Research
- Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School
- Justin B. Siegel
- Genome Center, University of California
- Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen
- Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, School of Medicine, University of California
- Brian Kuhlman
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill
- Andrew Leaver-Fay
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill
- Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1
- Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
- Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation
- DOI
- https://doi.org/10.1038/s41467-021-27222-7
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 15
Abstract
Computational methods are becoming an increasingly important part of biological research. Using the Rosetta framework as an example, the authors demonstrate how community-driven development of computational methods can be done in a reproducible and reliable fashion.
