Rosetta@home (Japanese Wikipedia)

“Rosetta@home”. 2022年3月14日閲覧。
“What is Rosetta@home?”. Rosetta@home forums. University of Washington. September 13, 2008時点のオリジナルよりアーカイブ。September 7, 2008閲覧。
“Help in the fight against COVID-19!”. Rosetta@home. 2020年4月13日閲覧。
“Coronavirus update from David Baker. Thank you all for your contributions!”. Rosetta@home. Rosetta@home (2020年9月21日). October 30, 2020時点のオリジナルよりアーカイブ。2020年9月23日閲覧。
“Another publication in Nature describing the first de novo designed proteins with anti-cancer activity”. Rosetta@home (2020年1月14日). October 19, 2020時点のオリジナルよりアーカイブ。2020年9月19日閲覧。
“Rosetta@home: Recommended System Requirements”. Rosetta@home. University of Washington (2008年). September 25, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Rosetta@home: News archive”. Rosetta@home. University of Washington (2016年). July 20, 2016閲覧。
“Rosetta@home: FAQ (work in progress) (message 10910)”. Rosetta@home forums. University of Washington (2006年). October 7, 2008閲覧。
Kim DE (2005年). “Rosetta@home: Random Seed (message 3155)”. Rosetta@home forums. University of Washington. October 7, 2008閲覧。
“Rosetta@home: Quick guide to Rosetta and its graphics”. Rosetta@home. University of Washington (2007年). September 24, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Rosetta@home: News archive”. Rosetta@home. University of Washington (2016年). July 20, 2016閲覧。
Kim DE (2008年). “Rosetta@home: Problems with minirosetta version 1.+ (Message 51199)”. Rosetta@home forums. University of Washington. September 7, 2008閲覧。
Baker D (2008年). “Rosetta@home: David Baker's Rosetta@home journal (message 55893)”. Rosetta@home forums. University of Washington. October 7, 2008閲覧。
“Rosetta@home: Research Overview”. Rosetta@home. University of Washington (2007年). September 25, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Disease Related Research”. Rosetta@home. University of Washington (2008年). September 23, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。
Baker D (2008年). “Rosetta@home: David Baker's Rosetta@home journal”. Rosetta@home forums. University of Washington. September 7, 2008閲覧。
“Rosetta@home Research Updates”. Boinc.bakerlab.org. 2014年4月18日閲覧。
“News archive”. Rosetta@home. May 10, 2019閲覧。
Bradley P. “Rosetta@home forum: Amyloid fibril structure prediction”. Rosetta@home forums. University of Washington. September 7, 2008閲覧。
Baker D. “Rosetta@home forum: Publications on R@H's Alzheimer's work? (message 54681)”. Rosetta@home forums. University of Washington. October 8, 2008閲覧。
Baker D. “David Baker's Rosetta@home journal archives (message 40756)”. Rosetta@home forums. University of Washington. September 7, 2008閲覧。
“Disease Related Research”. Rosetta@home. University of Washington (2008年). September 23, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。
“Another publication in Nature describing the first de novo designed proteins with anti-cancer activity”. Rosetta@home (2020年1月14日). 2020年9月19日閲覧。
“Rosetta@home: News archive”. Rosetta@home. University of Washington (2016年). July 20, 2016閲覧。
“Rosetta@home: Research Overview”. Rosetta@home. University of Washington (2007年). September 25, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Protein–protein docking at Rosetta@home”. Rosetta@home forums. University of Washington. September 7, 2008閲覧。
Baker D. “David Baker's Rosetta@home journal, message 52902”. Rosetta@home forums. University of Washington. September 7, 2008閲覧。
Baker D. “David Baker's Rosetta@home journal (message 52963)”. Rosetta@home forums. University of Washington. September 16, 2008閲覧。
“Rosetta@home”. 2020年3月19日閲覧。
“Rosetta@home: The new credit system explained”. Rosetta@home forums. University of Washington (2006年). October 8, 2008閲覧。
“Rosetta@home: Predictor of the day archive”. Rosetta@home. University of Washington (2008年). September 24, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。
“Rosetta@home: Protein Folding, Design, and Docking”. Rosetta@home. University of Washington (2008年). October 8, 2008閲覧。

bakerlab.org

“De novo minibinders target SARS-CoV-2 Spike protein”. Baker Lab. Baker Lab (2020年9月9日). 2020年9月19日閲覧。

ralph.bakerlab.org

“RALPH@home website”. RALPH@home forums. University of Washington. September 7, 2008閲覧。

berkeley.edu

boinc.berkeley.edu

“Download BOINC client software”. BOINC. University of California (2008年). December 1, 2008閲覧。
“Download BOINC client software”. BOINC. University of California (2008年). December 1, 2008閲覧。
“Project list – BOINC”. University of California. September 8, 2008閲覧。

boincstats.com

“Rosetta@home: Credit overview”. boincstats.com. 2020年3月28日閲覧。
“Rosetta@home: Credit overview”. boincstats.com. 2020年3月28日閲覧。
“BOINCstats: Project Credit Comparison”. boincstats.com (2008年). September 13, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。
“Credit divided over projects”. boincstats.com. February 19, 2015閲覧。

doi.org

Callaway E (July 2022). “The entire protein universe: AI predicts shape of nearly every known protein”. Nature 608: 15-16. doi:10.1038/d41586-022-02083-2.
Lensink MF, Méndez R, Wodak SJ (December 2007). “Docking and scoring protein complexes: CAPRI 3rd Edition”. Proteins 69 (4): 704–18. doi:10.1002/prot.21804. PMID 17918726.
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D (October 2020). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science 370 (6515): 426–431. Bibcode: 2020Sci...370..426C. doi:10.1126/science.abd9909. PMC 7857403. PMID 32907861.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T (2007). “Assessment of CASP7 predictions for template-based modeling targets”. Proteins 69 Suppl 8: 38–56. doi:10.1002/prot.21753. PMID 17894352.
Read RJ, Chavali G (2007). “Assessment of CASP7 predictions in the high accuracy template-based modeling category”. Proteins 69 Suppl 8: 27–37. doi:10.1002/prot.21662. PMID 17894351.
Jauch R, Yeo HC, Kolatkar PR, Clarke ND (2007). “Assessment of CASP7 structure predictions for template free targets”. Proteins 69 Suppl 8: 57–67. doi:10.1002/prot.21771. PMID 17894330.
Das R, Qian B, Raman S, etal (2007). “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home”. Proteins 69 Suppl 8: 118–28. doi:10.1002/prot.21636. PMID 17894356.
Wang C, Schueler-Furman O, Andre I, etal (December 2007). “RosettaDock in CAPRI rounds 6–12”. Proteins 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Hayden EC (February 13, 2008). “Protein prize up for grabs after retraction”. Nature. doi:10.1038/news.2008.569.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Kuhlman B, Baker D (September 2000). “Native protein sequences are close to optimal for their structures”. Proceedings of the National Academy of Sciences of the United States of America 97 (19): 10383–88. Bibcode: 2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D (March 2006). “The 3D profile method for identifying fibril-forming segments of proteins”. Proceedings of the National Academy of Sciences of the United States of America 103 (11): 4074–78. Bibcode: 2006PNAS..103.4074T. doi:10.1073/pnas.0511295103. PMC 1449648. PMID 16537487.
Wang C, Schueler-Furman O, Baker D (May 2005). “Improved side-chain modeling for protein–protein docking”. Protein Science 14 (5): 1328–39. doi:10.1110/ps.041222905. PMC 2253276. PMID 15802647.
Gray JJ, Moughon S, Wang C, etal (August 2003). “Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations”. Journal of Molecular Biology 331 (1): 281–99. doi:10.1016/S0022-2836(03)00670-3. PMID 12875852.
Schueler-Furman O, Wang C, Baker D (August 2005). “Progress in protein–protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility”. Proteins 60 (2): 187–94. doi:10.1002/prot.20556. PMID 15981249.
Lacy DB, Lin HC, Melnyk RA, etal (November 2005). “A model of anthrax toxin lethal factor bound to protective antigen”. Proceedings of the National Academy of Sciences of the United States of America 102 (45): 16409–14. Bibcode: 2005PNAS..10216409L. doi:10.1073/pnas.0508259102. PMC 1283467. PMID 16251269.
Albrecht MT, Li H, Williamson ED, etal (November 2007). “Human monoclonal antibodies against anthrax lethal factor and protective antigen act independently to protect against Bacillus anthracis infection and enhance endogenous immunity to anthrax”. Infection and Immunity 75 (11): 5425–33. doi:10.1128/IAI.00261-07. PMC 2168292. PMID 17646360.
Sprague ER, Wang C, Baker D, Bjorkman PJ (June 2006). “Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging”. PLOS Biology 4 (6): e148. doi:10.1371/journal.pbio.0040148. PMC 1450327. PMID 16646632.
Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A (2007). “Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos”. Nucleic Acids Research 35 (17): 5922–33. doi:10.1093/nar/gkm632. PMC 2034484. PMID 17726053.
Ashworth J, Havranek JJ, Duarte CM, etal (June 2006). “Computational redesign of endonuclease DNA binding and cleavage specificity”. Nature 441 (7093): 656–59. Bibcode: 2006Natur.441..656A. doi:10.1038/nature04818. PMC 2999987. PMID 16738662.
Cao, Longxing (2020-09-09). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science: eabd9909. doi:10.1126/science.abd9909. PMID 32907861.
Case JB, Chen RE, Cao L, Ying B, Winkler ES, Johnson M, Goreshnik I, Pham MN, Shrihari S, Kafai NM, Bailey AL, Xie X, Shi PY, Ravichandran R, Carter L, Stewart L, Baker D, Diamond MS (July 2021). “Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease” (English). Cell Host & Microbe 29 (7): 1151–1161.e5. doi:10.1016/j.chom.2021.06.008. PMC 8221914. PMID 34192518.
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SP, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D (July 2021). “Multivalent designed proteins protect against SARS-CoV-2 variants of concern”. bioRxiv: 2021.07.07.451375. doi:10.1101/2021.07.07.451375. PMC 8282097. PMID 34268509.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Simons KT, Bonneau R, Ruczinski I, Baker D (1999). “Ab initio protein structure prediction of CASP III targets using Rosetta”. Proteins Suppl 3: 171–76. doi:10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z. PMID 10526365.
Nauli S, Kuhlman B, Baker D (July 2001). “Computer-based redesign of a protein folding pathway”. Nature Structural Biology 8 (7): 602–05. doi:10.1038/89638. PMID 11427890.
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (November 2003). “Design of a novel globular protein fold with atomic-level accuracy”. Science 302 (5649): 1364–68. Bibcode: 2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033.
Jones DT (November 2003). “Structural biology. Learning to speak the language of proteins”. Science 302 (5649): 1347–48. doi:10.1126/science.1092492. PMID 14631028.
von Grotthuss M, Wyrwicz LS, Pas J, Rychlewski L (June 2004). “Predicting protein structures accurately”. Science 304 (5677): 1597–99; author reply 1597–99. doi:10.1126/science.304.5677.1597b. PMID 15192202.
Gray JJ, Moughon SE, Kortemme T, etal (July 2003). “Protein–protein docking predictions for the CAPRI experiment”. Proteins 52 (1): 118–22. doi:10.1002/prot.10384. PMID 12784377.
Gray JJ, Moughon SE, Kortemme T, etal (July 2003). “Protein–protein docking predictions for the CAPRI experiment”. Proteins 52 (1): 118–22. doi:10.1002/prot.10384. PMID 12784377.
Schueler-Furman O, Wang C, Baker D (August 2005). “Progress in protein–protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility”. Proteins 60 (2): 187–94. doi:10.1002/prot.20556. PMID 15981249.
Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ (2005). “CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock”. Proteins 60 (2): 181–86. doi:10.1002/prot.20555. PMID 15981262.
Méndez R, Leplae R, Lensink MF, Wodak SJ (2005). “Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures”. Proteins 60 (2): 150–69. doi:10.1002/prot.20551. PMID 15981261.
Lensink MF, Méndez R, Wodak SJ (December 2007). “Docking and scoring protein complexes: CAPRI 3rd Edition”. Proteins 69 (4): 704–18. doi:10.1002/prot.21804. PMID 17918726.
Wang C, Schueler-Furman O, Andre I, etal (December 2007). “RosettaDock in CAPRI rounds 6–12”. Proteins 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979.
Aloy P, Stark A, Hadley C, Russell RB (2003). “Predictions without templates: new folds, secondary structure, and contacts in CASP5”. Proteins 53 Suppl 6: 436–56. doi:10.1002/prot.10546. PMID 14579333.
Jauch R, Yeo HC, Kolatkar PR, Clarke ND (2007). “Assessment of CASP7 structure predictions for template free targets”. Proteins 69 Suppl 8: 57–67. doi:10.1002/prot.21771. PMID 17894330.
Tress M, Ezkurdia I, Graña O, López G, Valencia A (2005). “Assessment of predictions submitted for the CASP6 comparative modeling category”. Proteins 61 Suppl 7: 27–45. doi:10.1002/prot.20720. PMID 16187345.
Battey JN, Kopp J, Bordoli L, Read RJ, Clarke ND, Schwede T (2007). “Automated server predictions in CASP7”. Proteins 69 Suppl 8: 68–82. doi:10.1002/prot.21761. PMID 17894354.
Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D (2005). “Prediction of CASP6 structures using automated Robetta protocols”. Proteins 61 Suppl 7: 157–66. doi:10.1002/prot.20733. PMID 16187358.
Das R, Qian B, Raman S, etal (2007). “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home”. Proteins 69 Suppl 8: 118–28. doi:10.1002/prot.21636. PMID 17894356.
Ovchinnikov, S; Kim, DE; Wang, RY; Liu, Y; DiMaio, F; Baker, D (September 2016). “Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.”. Proteins 84 Suppl 1: 67–75. doi:10.1002/prot.24974. PMC 5490371. PMID 26677056.
Malmström L, Riffle M, Strauss CE, etal (April 2007). “Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology”. PLOS Biology 5 (4): e76. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.
Das R, Qian B, Raman S, etal (2007). “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home”. Proteins 69 Suppl 8: 118–28. doi:10.1002/prot.21636. PMID 17894356.

europepmc.org

Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ (2005). “CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock”. Proteins 60 (2): 181–86. doi:10.1002/prot.20555. PMID 15981262.
Méndez R, Leplae R, Lensink MF, Wodak SJ (2005). “Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures”. Proteins 60 (2): 150–69. doi:10.1002/prot.20551. PMID 15981261.

fah-addict.net

en.fah-addict.net

jmn (July 29, 2011). “Rosetta@home and Folding@home: additional projects”. September 19, 2011閲覧。

fold.it

“Foldit forums: How many users does Foldit have? Etc. (message 2)”. University of Washington. September 27, 2008閲覧。
“Foldit: Frequently Asked Questions”. fold.it. University of Washington. September 19, 2008閲覧。

foldingforum.org

7im (April 2, 2010). “Re: Answers to: Reasons for not using F@H”. September 19, 2011閲覧。
tjlane (June 9, 2011). “Re: Course grained Protein folding in under 10 minutes”. September 19, 2011閲覧。
tjlane (June 9, 2011). “Re: Course grained Protein folding in under 10 minutes”. September 19, 2011閲覧。

gcgh.org

“Homing Endonuclease Genes: New Tools for Mosquito Population Engineering and Control”. Grand Challenges in Global Health. September 7, 2008閲覧。

harvard.edu

ui.adsabs.harvard.edu

Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D (October 2020). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science 370 (6515): 426–431. Bibcode: 2020Sci...370..426C. doi:10.1126/science.abd9909. PMC 7857403. PMID 32907861.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Kuhlman B, Baker D (September 2000). “Native protein sequences are close to optimal for their structures”. Proceedings of the National Academy of Sciences of the United States of America 97 (19): 10383–88. Bibcode: 2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D (March 2006). “The 3D profile method for identifying fibril-forming segments of proteins”. Proceedings of the National Academy of Sciences of the United States of America 103 (11): 4074–78. Bibcode: 2006PNAS..103.4074T. doi:10.1073/pnas.0511295103. PMC 1449648. PMID 16537487.
Lacy DB, Lin HC, Melnyk RA, etal (November 2005). “A model of anthrax toxin lethal factor bound to protective antigen”. Proceedings of the National Academy of Sciences of the United States of America 102 (45): 16409–14. Bibcode: 2005PNAS..10216409L. doi:10.1073/pnas.0508259102. PMC 1283467. PMID 16251269.
Ashworth J, Havranek JJ, Duarte CM, etal (June 2006). “Computational redesign of endonuclease DNA binding and cleavage specificity”. Nature 441 (7093): 656–59. Bibcode: 2006Natur.441..656A. doi:10.1038/nature04818. PMC 2999987. PMID 16738662.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (November 2003). “Design of a novel globular protein fold with atomic-level accuracy”. Science 302 (5649): 1364–68. Bibcode: 2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033.

hivvaccineenterprise.org

Liu Y, etal (2007年). “Development of IgG1 b12 scaffolds and HIV-1 env-based outer domain immunogens capable of eliciting and detecting IgG1 b12-like antibodies”. Global HIV Vaccine Enterprise. February 25, 2009時点のオリジナルよりアーカイブ。September 28, 2008閲覧。

hpcwire.com

“Rosetta@home Rallies a Legion of Computers Against the Coronavirus”. HPCWire (2020年3月24日). 2020年3月25日閲覧。

neoleukin.com

investor.neoleukin.com

“Neoleukin Therapeutics Announces Initiation of Phase 1 NL-201 Trial | Neoleukin Therapeutics, Inc.” (英語). investor.neoleukin.com. June 24, 2021時点のオリジナルよりアーカイブ。2021年6月22日閲覧。
“Neoleukin Therapeutics Announces Submission of Investigational New Drug Application for NL-201 De Novo Protein Immunotherapy Candidate for Cancer”. Neoleukin Therapeutics (2020年12月10日). 2020年12月10日閲覧。

newyorker.com

Hutson, Matthew (2020年9月18日). “Scientists Advance on One of Technology's Holy Grails”. The New Yorker 2020年9月19日閲覧。

nih.gov

pubmed.ncbi.nlm.nih.gov

Lensink MF, Méndez R, Wodak SJ (December 2007). “Docking and scoring protein complexes: CAPRI 3rd Edition”. Proteins 69 (4): 704–18. doi:10.1002/prot.21804. PMID 17918726.
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D (October 2020). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science 370 (6515): 426–431. Bibcode: 2020Sci...370..426C. doi:10.1126/science.abd9909. PMC 7857403. PMID 32907861.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T (2007). “Assessment of CASP7 predictions for template-based modeling targets”. Proteins 69 Suppl 8: 38–56. doi:10.1002/prot.21753. PMID 17894352.
Read RJ, Chavali G (2007). “Assessment of CASP7 predictions in the high accuracy template-based modeling category”. Proteins 69 Suppl 8: 27–37. doi:10.1002/prot.21662. PMID 17894351.
Jauch R, Yeo HC, Kolatkar PR, Clarke ND (2007). “Assessment of CASP7 structure predictions for template free targets”. Proteins 69 Suppl 8: 57–67. doi:10.1002/prot.21771. PMID 17894330.
Das R, Qian B, Raman S, etal (2007). “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home”. Proteins 69 Suppl 8: 118–28. doi:10.1002/prot.21636. PMID 17894356.
Wang C, Schueler-Furman O, Andre I, etal (December 2007). “RosettaDock in CAPRI rounds 6–12”. Proteins 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Kuhlman B, Baker D (September 2000). “Native protein sequences are close to optimal for their structures”. Proceedings of the National Academy of Sciences of the United States of America 97 (19): 10383–88. Bibcode: 2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D (March 2006). “The 3D profile method for identifying fibril-forming segments of proteins”. Proceedings of the National Academy of Sciences of the United States of America 103 (11): 4074–78. Bibcode: 2006PNAS..103.4074T. doi:10.1073/pnas.0511295103. PMC 1449648. PMID 16537487.
Wang C, Schueler-Furman O, Baker D (May 2005). “Improved side-chain modeling for protein–protein docking”. Protein Science 14 (5): 1328–39. doi:10.1110/ps.041222905. PMC 2253276. PMID 15802647.
Gray JJ, Moughon S, Wang C, etal (August 2003). “Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations”. Journal of Molecular Biology 331 (1): 281–99. doi:10.1016/S0022-2836(03)00670-3. PMID 12875852.
Schueler-Furman O, Wang C, Baker D (August 2005). “Progress in protein–protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility”. Proteins 60 (2): 187–94. doi:10.1002/prot.20556. PMID 15981249.
Lacy DB, Lin HC, Melnyk RA, etal (November 2005). “A model of anthrax toxin lethal factor bound to protective antigen”. Proceedings of the National Academy of Sciences of the United States of America 102 (45): 16409–14. Bibcode: 2005PNAS..10216409L. doi:10.1073/pnas.0508259102. PMC 1283467. PMID 16251269.
Albrecht MT, Li H, Williamson ED, etal (November 2007). “Human monoclonal antibodies against anthrax lethal factor and protective antigen act independently to protect against Bacillus anthracis infection and enhance endogenous immunity to anthrax”. Infection and Immunity 75 (11): 5425–33. doi:10.1128/IAI.00261-07. PMC 2168292. PMID 17646360.
Sprague ER, Wang C, Baker D, Bjorkman PJ (June 2006). “Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging”. PLOS Biology 4 (6): e148. doi:10.1371/journal.pbio.0040148. PMC 1450327. PMID 16646632.
Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A (2007). “Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos”. Nucleic Acids Research 35 (17): 5922–33. doi:10.1093/nar/gkm632. PMC 2034484. PMID 17726053.
Ashworth J, Havranek JJ, Duarte CM, etal (June 2006). “Computational redesign of endonuclease DNA binding and cleavage specificity”. Nature 441 (7093): 656–59. Bibcode: 2006Natur.441..656A. doi:10.1038/nature04818. PMC 2999987. PMID 16738662.
Cao, Longxing (2020-09-09). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science: eabd9909. doi:10.1126/science.abd9909. PMID 32907861.
Case JB, Chen RE, Cao L, Ying B, Winkler ES, Johnson M, Goreshnik I, Pham MN, Shrihari S, Kafai NM, Bailey AL, Xie X, Shi PY, Ravichandran R, Carter L, Stewart L, Baker D, Diamond MS (July 2021). “Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease” (English). Cell Host & Microbe 29 (7): 1151–1161.e5. doi:10.1016/j.chom.2021.06.008. PMC 8221914. PMID 34192518.
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SP, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D (July 2021). “Multivalent designed proteins protect against SARS-CoV-2 variants of concern”. bioRxiv: 2021.07.07.451375. doi:10.1101/2021.07.07.451375. PMC 8282097. PMID 34268509.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Simons KT, Bonneau R, Ruczinski I, Baker D (1999). “Ab initio protein structure prediction of CASP III targets using Rosetta”. Proteins Suppl 3: 171–76. doi:10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z. PMID 10526365.
Nauli S, Kuhlman B, Baker D (July 2001). “Computer-based redesign of a protein folding pathway”. Nature Structural Biology 8 (7): 602–05. doi:10.1038/89638. PMID 11427890.
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (November 2003). “Design of a novel globular protein fold with atomic-level accuracy”. Science 302 (5649): 1364–68. Bibcode: 2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033.
Jones DT (November 2003). “Structural biology. Learning to speak the language of proteins”. Science 302 (5649): 1347–48. doi:10.1126/science.1092492. PMID 14631028.
von Grotthuss M, Wyrwicz LS, Pas J, Rychlewski L (June 2004). “Predicting protein structures accurately”. Science 304 (5677): 1597–99; author reply 1597–99. doi:10.1126/science.304.5677.1597b. PMID 15192202.
Gray JJ, Moughon SE, Kortemme T, etal (July 2003). “Protein–protein docking predictions for the CAPRI experiment”. Proteins 52 (1): 118–22. doi:10.1002/prot.10384. PMID 12784377.
Gray JJ, Moughon SE, Kortemme T, etal (July 2003). “Protein–protein docking predictions for the CAPRI experiment”. Proteins 52 (1): 118–22. doi:10.1002/prot.10384. PMID 12784377.
Schueler-Furman O, Wang C, Baker D (August 2005). “Progress in protein–protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility”. Proteins 60 (2): 187–94. doi:10.1002/prot.20556. PMID 15981249.
Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ (2005). “CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock”. Proteins 60 (2): 181–86. doi:10.1002/prot.20555. PMID 15981262.
Méndez R, Leplae R, Lensink MF, Wodak SJ (2005). “Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures”. Proteins 60 (2): 150–69. doi:10.1002/prot.20551. PMID 15981261.
Lensink MF, Méndez R, Wodak SJ (December 2007). “Docking and scoring protein complexes: CAPRI 3rd Edition”. Proteins 69 (4): 704–18. doi:10.1002/prot.21804. PMID 17918726.
Wang C, Schueler-Furman O, Andre I, etal (December 2007). “RosettaDock in CAPRI rounds 6–12”. Proteins 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979.
Aloy P, Stark A, Hadley C, Russell RB (2003). “Predictions without templates: new folds, secondary structure, and contacts in CASP5”. Proteins 53 Suppl 6: 436–56. doi:10.1002/prot.10546. PMID 14579333.
Jauch R, Yeo HC, Kolatkar PR, Clarke ND (2007). “Assessment of CASP7 structure predictions for template free targets”. Proteins 69 Suppl 8: 57–67. doi:10.1002/prot.21771. PMID 17894330.
Tress M, Ezkurdia I, Graña O, López G, Valencia A (2005). “Assessment of predictions submitted for the CASP6 comparative modeling category”. Proteins 61 Suppl 7: 27–45. doi:10.1002/prot.20720. PMID 16187345.
Battey JN, Kopp J, Bordoli L, Read RJ, Clarke ND, Schwede T (2007). “Automated server predictions in CASP7”. Proteins 69 Suppl 8: 68–82. doi:10.1002/prot.21761. PMID 17894354.
Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D (2005). “Prediction of CASP6 structures using automated Robetta protocols”. Proteins 61 Suppl 7: 157–66. doi:10.1002/prot.20733. PMID 16187358.
Das R, Qian B, Raman S, etal (2007). “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home”. Proteins 69 Suppl 8: 118–28. doi:10.1002/prot.21636. PMID 17894356.
Ovchinnikov, S; Kim, DE; Wang, RY; Liu, Y; DiMaio, F; Baker, D (September 2016). “Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.”. Proteins 84 Suppl 1: 67–75. doi:10.1002/prot.24974. PMC 5490371. PMID 26677056.
Malmström L, Riffle M, Strauss CE, etal (April 2007). “Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology”. PLOS Biology 5 (4): e76. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.
Das R, Qian B, Raman S, etal (2007). “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home”. Proteins 69 Suppl 8: 118–28. doi:10.1002/prot.21636. PMID 17894356.

ncbi.nlm.nih.gov

Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D (October 2020). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science 370 (6515): 426–431. Bibcode: 2020Sci...370..426C. doi:10.1126/science.abd9909. PMC 7857403. PMID 32907861.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Kuhlman B, Baker D (September 2000). “Native protein sequences are close to optimal for their structures”. Proceedings of the National Academy of Sciences of the United States of America 97 (19): 10383–88. Bibcode: 2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D (March 2006). “The 3D profile method for identifying fibril-forming segments of proteins”. Proceedings of the National Academy of Sciences of the United States of America 103 (11): 4074–78. Bibcode: 2006PNAS..103.4074T. doi:10.1073/pnas.0511295103. PMC 1449648. PMID 16537487.
Wang C, Schueler-Furman O, Baker D (May 2005). “Improved side-chain modeling for protein–protein docking”. Protein Science 14 (5): 1328–39. doi:10.1110/ps.041222905. PMC 2253276. PMID 15802647.
Lacy DB, Lin HC, Melnyk RA, etal (November 2005). “A model of anthrax toxin lethal factor bound to protective antigen”. Proceedings of the National Academy of Sciences of the United States of America 102 (45): 16409–14. Bibcode: 2005PNAS..10216409L. doi:10.1073/pnas.0508259102. PMC 1283467. PMID 16251269.
Albrecht MT, Li H, Williamson ED, etal (November 2007). “Human monoclonal antibodies against anthrax lethal factor and protective antigen act independently to protect against Bacillus anthracis infection and enhance endogenous immunity to anthrax”. Infection and Immunity 75 (11): 5425–33. doi:10.1128/IAI.00261-07. PMC 2168292. PMID 17646360.
Sprague ER, Wang C, Baker D, Bjorkman PJ (June 2006). “Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging”. PLOS Biology 4 (6): e148. doi:10.1371/journal.pbio.0040148. PMC 1450327. PMID 16646632.
Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A (2007). “Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos”. Nucleic Acids Research 35 (17): 5922–33. doi:10.1093/nar/gkm632. PMC 2034484. PMID 17726053.
Ashworth J, Havranek JJ, Duarte CM, etal (June 2006). “Computational redesign of endonuclease DNA binding and cleavage specificity”. Nature 441 (7093): 656–59. Bibcode: 2006Natur.441..656A. doi:10.1038/nature04818. PMC 2999987. PMID 16738662.
Case JB, Chen RE, Cao L, Ying B, Winkler ES, Johnson M, Goreshnik I, Pham MN, Shrihari S, Kafai NM, Bailey AL, Xie X, Shi PY, Ravichandran R, Carter L, Stewart L, Baker D, Diamond MS (July 2021). “Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease” (English). Cell Host & Microbe 29 (7): 1151–1161.e5. doi:10.1016/j.chom.2021.06.008. PMC 8221914. PMID 34192518.
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SP, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D (July 2021). “Multivalent designed proteins protect against SARS-CoV-2 variants of concern”. bioRxiv: 2021.07.07.451375. doi:10.1101/2021.07.07.451375. PMC 8282097. PMID 34268509.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Ovchinnikov, S; Kim, DE; Wang, RY; Liu, Y; DiMaio, F; Baker, D (September 2016). “Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.”. Proteins 84 Suppl 1: 67–75. doi:10.1002/prot.24974. PMC 5490371. PMID 26677056.
Malmström L, Riffle M, Strauss CE, etal (April 2007). “Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology”. PLOS Biology 5 (4): e76. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.

pmc.ncbi.nlm.nih.gov

Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D (October 2020). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science 370 (6515): 426–431. Bibcode: 2020Sci...370..426C. doi:10.1126/science.abd9909. PMC 7857403. PMID 32907861.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Jiang L, Althoff EA, Clemente FR, etal (March 2008). “De novo computational design of retro-aldol enzymes”. Science 319 (5868): 1387–91. Bibcode: 2008Sci...319.1387J. doi:10.1126/science.1152692. PMC 3431203. PMID 18323453.
Kuhlman B, Baker D (September 2000). “Native protein sequences are close to optimal for their structures”. Proceedings of the National Academy of Sciences of the United States of America 97 (19): 10383–88. Bibcode: 2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D (March 2006). “The 3D profile method for identifying fibril-forming segments of proteins”. Proceedings of the National Academy of Sciences of the United States of America 103 (11): 4074–78. Bibcode: 2006PNAS..103.4074T. doi:10.1073/pnas.0511295103. PMC 1449648. PMID 16537487.
Wang C, Schueler-Furman O, Baker D (May 2005). “Improved side-chain modeling for protein–protein docking”. Protein Science 14 (5): 1328–39. doi:10.1110/ps.041222905. PMC 2253276. PMID 15802647.
Lacy DB, Lin HC, Melnyk RA, etal (November 2005). “A model of anthrax toxin lethal factor bound to protective antigen”. Proceedings of the National Academy of Sciences of the United States of America 102 (45): 16409–14. Bibcode: 2005PNAS..10216409L. doi:10.1073/pnas.0508259102. PMC 1283467. PMID 16251269.
Albrecht MT, Li H, Williamson ED, etal (November 2007). “Human monoclonal antibodies against anthrax lethal factor and protective antigen act independently to protect against Bacillus anthracis infection and enhance endogenous immunity to anthrax”. Infection and Immunity 75 (11): 5425–33. doi:10.1128/IAI.00261-07. PMC 2168292. PMID 17646360.
Sprague ER, Wang C, Baker D, Bjorkman PJ (June 2006). “Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging”. PLOS Biology 4 (6): e148. doi:10.1371/journal.pbio.0040148. PMC 1450327. PMID 16646632.
Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A (2007). “Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos”. Nucleic Acids Research 35 (17): 5922–33. doi:10.1093/nar/gkm632. PMC 2034484. PMID 17726053.
Ashworth J, Havranek JJ, Duarte CM, etal (June 2006). “Computational redesign of endonuclease DNA binding and cleavage specificity”. Nature 441 (7093): 656–59. Bibcode: 2006Natur.441..656A. doi:10.1038/nature04818. PMC 2999987. PMID 16738662.
Case JB, Chen RE, Cao L, Ying B, Winkler ES, Johnson M, Goreshnik I, Pham MN, Shrihari S, Kafai NM, Bailey AL, Xie X, Shi PY, Ravichandran R, Carter L, Stewart L, Baker D, Diamond MS (July 2021). “Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease” (English). Cell Host & Microbe 29 (7): 1151–1161.e5. doi:10.1016/j.chom.2021.06.008. PMC 8221914. PMID 34192518.
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SP, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D (July 2021). “Multivalent designed proteins protect against SARS-CoV-2 variants of concern”. bioRxiv: 2021.07.07.451375. doi:10.1101/2021.07.07.451375. PMC 8282097. PMID 34268509.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJ, Dougan M, Garcia KC, Baker D (January 2019). “De novo design of potent and selective mimics of IL-2 and IL-15.”. Nature 565 (7738): 186–191. Bibcode: 2019Natur.565..186S. doi:10.1038/s41586-018-0830-7. PMC 6521699. PMID 30626941.
Ovchinnikov, S; Kim, DE; Wang, RY; Liu, Y; DiMaio, F; Baker, D (September 2016). “Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.”. Proteins 84 Suppl 1: 67–75. doi:10.1002/prot.24974. PMC 5490371. PMID 26677056.
Malmström L, Riffle M, Strauss CE, etal (April 2007). “Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology”. PLOS Biology 5 (4): e76. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.

nyu.edu

homepages.nyu.edu

Bonneau R (2006年). “World Community Grid Message Board Posts: HPF -> HPF2 transition”. Bonneau Lab, New York University. September 7, 2008閲覧。
“List of Richard Bonneau's publications”. Bonneau Lab, New York University. July 7, 2008時点のオリジナルよりアーカイブ。September 7, 2008閲覧。
Bonneau R. “World Community Grid Message Board Posts”. Bonneau Lab, New York University. July 4, 2008時点のオリジナルよりアーカイブ。September 7, 2008閲覧。

pdb.org

“Yearly Growth of Protein Structures”. RCSB Protein Data Bank (2008年). November 30, 2008閲覧。
“October 2005 molecule of the month: Designer proteins”. RCSB Protein Data Bank. September 7, 2008閲覧。

reuters.com

“S. Korea approves Phase III trial of SK Bioscience's COVID-19 vaccine” (英語). Reuters (2021年8月10日). August 18, 2021時点のオリジナルよりアーカイブ。2021年8月18日閲覧。

robetta.org

new.robetta.org

“Robetta web server”. Baker laboratory. University of Washington. May 7, 2019閲覧。

rosettacommons.org

“Rosetta Commons”. RosettaCommons.org (2008年). September 15, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。

rosie.rosettacommons.org

“RosettaDock server”. Rosetta Commons. March 28, 2020閲覧。

sciencemag.org

science.sciencemag.org

Cao, Longxing (2020-09-09). “De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”. Science: eabd9909. doi:10.1126/science.abd9909. PMID 32907861.

sciencemag.org

“Articles citing: Kuhlman et al. (2003) 'Design of a novel globular protein fold with atomic-level accuracy'”. ISI Web of Science. July 10, 2008閲覧。

scripps.edu

Carrillo-Tripp M (2007年). “dTASSER”. The Scripps Research Institute. July 6, 2007時点のオリジナルよりアーカイブ。September 7, 2008閲覧。

seattlepi.com

Paulson, Tom (July 19, 2006). “Gates Foundation awards $287 million for HIV vaccine research”. Seattle Post-Intelligencer September 7, 2008閲覧。

stanford.edu

folding.stanford.edu

Pande Group (2010年). “High Performance FAQ” (FAQ). Stanford University. September 21, 2012時点のオリジナルよりアーカイブ。September 19, 2011閲覧。
Pande Group. “Folding@home Diseases Studied FAQ” (FAQ). Stanford University. October 11, 2007時点のオリジナルよりアーカイブ。September 12, 2011閲覧。

fah-web.stanford.edu

Pande Group. “Client Statistics by OS”. Stanford University. October 18, 2011閲覧。

teampicard.com

“Interview with David Baker”. Team Picard Distributed Computing (2006年). February 18, 2009時点のオリジナルよりアーカイブ。December 23, 2008閲覧。

twitter.com

Rosetta@home (2021年6月25日). “The COVID-19 projects on our platform are headed into human clinical trials! Our amazing online volunteers have played a role in the development of a promising new vaccine as well as candidate antiviral treatments.” (英語). Twitter. June 26, 2021時点のオリジナルよりアーカイブ。2021年6月26日閲覧。
Institute of Protein Design (2021年8月10日). “Archived copy” (英語). Twitter. August 18, 2021時点のオリジナルよりアーカイブ。2021年8月18日閲覧。
“Coronavirus Research Update”. Rosetta@home Official Twitter. Rosetta@Home (2020年6月26日). 2020年6月27日閲覧。
“Big news out of @UWproteindesign: a new candidate treatment for #COVID19! More lab testing still needed. Thanks to all the volunteers who helped crunch data for this project!!”. Rosetta@home Twitter. Rosetta@home Twitter (2020年9月9日). 2020年9月19日閲覧。

typepad.com

folding.typepad.com

Vijay Pande (August 5, 2011). “Results page updated – new key result published in our work in Alzheimer's Disease”. September 19, 2011閲覧。
Vijay Pande (September 26, 2007). “How FAH works: Molecular dynamics”. September 10, 2011閲覧。

umich.edu

predictor.chem.lsa.umich.edu

“Predictor@home: Developing new application areas for P@H”. The Brooks Research Group. September 7, 2008閲覧。^{[リンク切れ]}

unc.edu

“Kuhlman laboratory homepage”. Kuhlman Laboratory. University of North Carolina. September 7, 2008閲覧。

rosettadesign.med.unc.edu

“RosettaDesign web server”. Kuhlman Laboratory. University of North Carolina. September 7, 2008閲覧。

uw.edu

ipd.uw.edu

“IPD Annual Report 2021”. Institute for Protein Design (2021年7月14日). August 18, 2021時点のオリジナルよりアーカイブ。2021年8月18日閲覧。
“Rosetta's role in fighting coronavirus – Institute for Protein Design” (英語). 2020年3月6日閲覧。

web.archive.org

“What is Rosetta@home?”. Rosetta@home forums. University of Washington. September 13, 2008時点のオリジナルよりアーカイブ。September 7, 2008閲覧。
Rosetta@home (2021年6月25日). “The COVID-19 projects on our platform are headed into human clinical trials! Our amazing online volunteers have played a role in the development of a promising new vaccine as well as candidate antiviral treatments.” (英語). Twitter. June 26, 2021時点のオリジナルよりアーカイブ。2021年6月26日閲覧。
“Coronavirus update from David Baker. Thank you all for your contributions!”. Rosetta@home. Rosetta@home (2020年9月21日). October 30, 2020時点のオリジナルよりアーカイブ。2020年9月23日閲覧。
“IPD Annual Report 2021”. Institute for Protein Design (2021年7月14日). August 18, 2021時点のオリジナルよりアーカイブ。2021年8月18日閲覧。
“ANZCTR - Registration”. anzctr.org.au. October 30, 2021時点のオリジナルよりアーカイブ。2021年7月9日閲覧。
“S. Korea approves Phase III trial of SK Bioscience's COVID-19 vaccine” (英語). Reuters (2021年8月10日). August 18, 2021時点のオリジナルよりアーカイブ。2021年8月18日閲覧。
Institute of Protein Design (2021年8月10日). “Archived copy” (英語). Twitter. August 18, 2021時点のオリジナルよりアーカイブ。2021年8月18日閲覧。
“Neoleukin Therapeutics Announces Initiation of Phase 1 NL-201 Trial | Neoleukin Therapeutics, Inc.” (英語). investor.neoleukin.com. June 24, 2021時点のオリジナルよりアーカイブ。2021年6月22日閲覧。
“Another publication in Nature describing the first de novo designed proteins with anti-cancer activity”. Rosetta@home (2020年1月14日). October 19, 2020時点のオリジナルよりアーカイブ。2020年9月19日閲覧。
“Rosetta@home: Recommended System Requirements”. Rosetta@home. University of Washington (2008年). September 25, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Rosetta@home: Quick guide to Rosetta and its graphics”. Rosetta@home. University of Washington (2007年). September 24, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Rosetta Commons”. RosettaCommons.org (2008年). September 15, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Rosetta@home: Research Overview”. Rosetta@home. University of Washington (2007年). September 25, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
“Disease Related Research”. Rosetta@home. University of Washington (2008年). September 23, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。
Liu Y, etal (2007年). “Development of IgG1 b12 scaffolds and HIV-1 env-based outer domain immunogens capable of eliciting and detecting IgG1 b12-like antibodies”. Global HIV Vaccine Enterprise. February 25, 2009時点のオリジナルよりアーカイブ。September 28, 2008閲覧。
“Disease Related Research”. Rosetta@home. University of Washington (2008年). September 23, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。
“Interview with David Baker”. Team Picard Distributed Computing (2006年). February 18, 2009時点のオリジナルよりアーカイブ。December 23, 2008閲覧。
“Rosetta@home: Research Overview”. Rosetta@home. University of Washington (2007年). September 25, 2008時点のオリジナルよりアーカイブ。October 7, 2008閲覧。
Pande Group. “Folding@home Diseases Studied FAQ” (FAQ). Stanford University. October 11, 2007時点のオリジナルよりアーカイブ。September 12, 2011閲覧。
“List of Richard Bonneau's publications”. Bonneau Lab, New York University. July 7, 2008時点のオリジナルよりアーカイブ。September 7, 2008閲覧。
Bonneau R. “World Community Grid Message Board Posts”. Bonneau Lab, New York University. July 4, 2008時点のオリジナルよりアーカイブ。September 7, 2008閲覧。
Carrillo-Tripp M (2007年). “dTASSER”. The Scripps Research Institute. July 6, 2007時点のオリジナルよりアーカイブ。September 7, 2008閲覧。
“BOINCstats: Project Credit Comparison”. boincstats.com (2008年). September 13, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。
“Rosetta@home: Predictor of the day archive”. Rosetta@home. University of Washington (2008年). September 24, 2008時点のオリジナルよりアーカイブ。October 8, 2008閲覧。

webcitation.org

Pande Group (2010年). “High Performance FAQ” (FAQ). Stanford University. September 21, 2012時点のオリジナルよりアーカイブ。September 19, 2011閲覧。