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RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

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Cited by:

  1. repec:plo:pbio00:3000919 is not listed on IDEAS
  2. Jared Adolf-Bryfogle & Oleks Kalyuzhniy & Michael Kubitz & Brian D Weitzner & Xiaozhen Hu & Yumiko Adachi & William R Schief & Roland L Dunbrack Jr., 2018. "RosettaAntibodyDesign (RAbD): A general framework for computational antibody design," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-38, April.
  3. Carla P. Perez & Nicole V. DelRosso & Cameron L. Noland & Udit Parekh & Christian A. Choe & Raphael R. Eguchi & Qi Wen & Polly M. Fordyce & Po-Ssu Huang, 2026. "ADAPT-M: a workflow for rapid, quantitative in vitro measurements of enriched protein libraries," Nature Communications, Nature, vol. 17(1), pages 1-17, December.
  4. Daniel Ellis & Julia Lederhofer & Oliver J. Acton & Yaroslav Tsybovsky & Sally Kephart & Christina Yap & Rebecca A. Gillespie & Adrian Creanga & Audrey Olshefsky & Tyler Stephens & Deleah Pettie & Mic, 2022. "Structure-based design of stabilized recombinant influenza neuraminidase tetramers," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  5. Julia Skokowa & Birte Hernandez Alvarez & Murray Coles & Malte Ritter & Masoud Nasri & Jérémy Haaf & Narges Aghaallaei & Yun Xu & Perihan Mir & Ann-Christin Krahl & Katherine W. Rogers & Kateryna Maks, 2022. "A topological refactoring design strategy yields highly stable granulopoietic proteins," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  6. Yoko Fujita-Fujiharu & Shangfan Hu & Ai Hirabayashi & Yuki Takamatsu & Yen Ni Ng & Kazuya Houri & Yukiko Muramoto & Masahiro Nakano & Yukihiko Sugita & Takeshi Noda, 2025. "Structural basis for Ebola virus nucleocapsid assembly and function regulated by VP24," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  7. Vishruth Mullapudi & Jaime Vaquer-Alicea & Vaibhav Bommareddy & Anthony R. Vega & Bryan D. Ryder & Charles L. White & Marc. I. Diamond & Lukasz A. Joachimiak, 2023. "Network of hotspot interactions cluster tau amyloid folds," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  8. Blanca Poquet & Galal Yahya & Laia Ferrer & Enrique Marcos & Carme Gallego & Martí Aldea, 2026. "Highly dynamic assemblies of glycolytic enzymes by quinary determinants," Nature Communications, Nature, vol. 17(1), pages 1-13, December.
  9. Thomas W. Linsky & Kyle Noble & Autumn R. Tobin & Rachel Crow & Lauren Carter & Jeffrey L. Urbauer & David Baker & Eva-Maria Strauch, 2022. "Sampling of structure and sequence space of small protein folds," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  10. Kristin J. Adolfsen & Isolde Callihan & Catherine E. Monahan & Per Jr. Greisen & James Spoonamore & Munira Momin & Lauren E. Fitch & Mary Joan Castillo & Lindong Weng & Lauren Renaud & Carl J. Weile &, 2021. "Improvement of a synthetic live bacterial therapeutic for phenylketonuria with biosensor-enabled enzyme engineering," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  11. Zachary R. Crook & Gregory P. Sevilla & Pamela Young & Emily J. Girard & Tinh-Doan Phi & Monique L. Howard & Jason Price & James M. Olson & Natalie W. Nairn, 2024. "CYpHER: catalytic extracellular targeted protein degradation with high potency and durable effect," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  12. Karen J. Gonzalez & Jiachen Huang & Miria F. Criado & Avik Banerjee & Stephen M. Tompkins & Jarrod J. Mousa & Eva-Maria Strauch, 2024. "A general computational design strategy for stabilizing viral class I fusion proteins," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  13. Tamuka M. Chidyausiku & Soraia R. Mendes & Jason C. Klima & Marta Nadal & Ulrich Eckhard & Jorge Roel-Touris & Scott Houliston & Tibisay Guevara & Hugh K. Haddox & Adam Moyer & Cheryl H. Arrowsmith & , 2022. "De novo design of immunoglobulin-like domains," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  14. Jaume Bonet & Sarah Wehrle & Karen Schriever & Che Yang & Anne Billet & Fabian Sesterhenn & Andreas Scheck & Freyr Sverrisson & Barbora Veselkova & Sabrina Vollers & Roxanne Lourman & Mélanie Villard , 2018. "Rosetta FunFolDes – A general framework for the computational design of functional proteins," PLOS Computational Biology, Public Library of Science, vol. 14(11), pages 1-30, November.
  15. Yanan Zhu & Alex B. Kleinpeter & Juan S. Rey & Juan Shen & Yao Shen & Jialu Xu & Nathan Hardenbrook & Long Chen & Anka Lucic & Juan R. Perilla & Eric O. Freed & Peijun Zhang, 2025. "Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  16. William G. Arndt & Alireza Ramezani & Nathaniel Talledge & Guichuan Yu & Huixin Yang & Bo Chen & Juan R. Perilla & Wei Zhang & Louis M. Mansky, 2026. "High-resolution analysis of the human T-cell leukemia virus capsid protein reveals insights into immature particle morphology," Nature Communications, Nature, vol. 17(1), pages 1-12, December.
  17. Jonathan Yaacov Weinstein & Carlos Martí-Gómez & Rosalie Lipsh-Sokolik & Shlomo Yakir Hoch & Demian Liebermann & Reinat Nevo & Haim Weissman & Ekaterina Petrovich-Kopitman & David Margulies & Dmitry I, 2023. "Designed active-site library reveals thousands of functional GFP variants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  18. P. Konstantin Richter & Paula Blázquez-Sánchez & Ziyue Zhao & Felipe Engelberger & Christian Wiebeler & Georg Künze & Ronny Frank & Dana Krinke & Emanuele Frezzotti & Yuliia Lihanova & Patricia Falken, 2023. "Structure and function of the metagenomic plastic-degrading polyester hydrolase PHL7 bound to its product," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  19. Edward King & Sarah Maxel & Yulai Zhang & Karissa C. Kenney & Youtian Cui & Emma Luu & Justin B. Siegel & Gregory A. Weiss & Ray Luo & Han Li, 2022. "Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  20. Xinlei Zhuang & Zhe Wang & Jiansheng Fan & Xuefei Bai & Yingchun Xu & James J. Chou & Tingjun Hou & Shuqing Chen & Liqiang Pan, 2022. "Structure-guided and phage-assisted evolution of a therapeutic anti-EGFR antibody to reverse acquired resistance," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  21. Diego del Alamo & Kevin L Jagessar & Jens Meiler & Hassane S Mchaourab, 2021. "Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints," PLOS Computational Biology, Public Library of Science, vol. 17(6), pages 1-18, June.
  22. Sowmiya Palani & Yuka Machida & Julia R. Alvey & Vandana Mishra & Allison L. Welter & Gaofeng Cui & Benoît Bragantini & Maria Victoria Botuyan & Anh T. Q. Cong & Georges Mer & Matthew J. Schellenberg , 2024. "Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  23. Nadav Elad & Zhen Hou & Maud Dumoux & Alireza Ramezani & Juan R. Perilla & Peijun Zhang, 2025. "In-cell structure and variability of pyrenoid Rubisco," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  24. Jorge Roel-Touris & Marta Nadal & Enrique Marcos, 2023. "Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  25. Qijia Wei & Dangliang Liu & Wencheng Xia & Fengzhang Wang & Lu Huang & Jun Zhang & Xiaoya Wang & Zhongxin Xu & Changdong He & Wenzhe Li & Xiaomeng Shi & Chu Wang & Yuan Liu & Cong Liu & Suwei Dong, 2025. "An O-glycopeptide participates in the formation of distinct Aβ42 fibril structures and attenuates Aβ42 neurotoxicity," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  26. Alexander M Sevy & Tim M Jacobs & James E Crowe Jr. & Jens Meiler, 2015. "Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-23, July.
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