Rosetta@home (English Wikipedia)

"Rosetta@home License Agreement". Boinc.bakerlab.org. Archived from the original on June 12, 2020. Retrieved October 27, 2024.
"Rosetta@home". Archived from the original on August 7, 2024. Retrieved September 23, 2024.
"Rosetta@home". Archived from the original on March 14, 2016. Retrieved March 24, 2020.
"What is Rosetta@home?". Rosetta@home forums. University of Washington. Archived from the original on September 13, 2008. Retrieved September 7, 2008.
"Rosetta@home - Server Status "TeraFLOPS estimate"". Rosetta@home. March 28, 2020. Archived from the original on January 3, 2016. Retrieved March 28, 2020.
"Coronavirus update from David Baker. Thank you all for your contributions!". Rosetta@home. September 21, 2020. Archived from the original on October 30, 2020. Retrieved September 23, 2020.
"Another publication in Nature describing the first de novo designed proteins with anti-cancer activity". Rosetta@home. January 14, 2020. Archived from the original on October 19, 2020. Retrieved September 19, 2020.
"Rosetta@home: Recommended System Requirements". Rosetta@home. University of Washington. 2008. Archived from the original on September 25, 2008. Retrieved October 7, 2008.
"Rosetta@home: News archive". Rosetta@home. University of Washington. 2016. Archived from the original on June 16, 2016. Retrieved July 20, 2016.
"Rosetta@home: FAQ (work in progress) (message 10910)". Rosetta@home forums. University of Washington. 2006. Archived from the original on February 26, 2009. Retrieved October 7, 2008.
Kim DE (2005). "Rosetta@home: Random Seed (message 3155)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved October 7, 2008.
"Rosetta@home: Quick guide to Rosetta and its graphics". Rosetta@home. University of Washington. 2007. Archived from the original on September 24, 2008. Retrieved October 7, 2008.
Baker D (2008). "Rosetta@home: David Baker's Rosetta@home journal (message 55893)". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved October 7, 2008.
"Rosetta@home: Research Overview". Rosetta@home. University of Washington. 2007. Archived from the original on September 25, 2008. Retrieved October 7, 2008.
"Disease Related Research". Rosetta@home. University of Washington. 2008. Archived from the original on September 23, 2008. Retrieved October 8, 2008.
Baker D (2008). "Rosetta@home: David Baker's Rosetta@home journal". Rosetta@home forums. University of Washington. Archived from the original on September 25, 2008. Retrieved September 7, 2008.
"Rosetta@home Research Updates". Boinc.bakerlab.org. Archived from the original on April 19, 2014. Retrieved April 18, 2014.
"News archive". Rosetta@home. Archived from the original on May 10, 2019. Retrieved May 10, 2019.
Bradley P. "Rosetta@home forum: Amyloid fibril structure prediction". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved September 7, 2008.
Baker D. "Rosetta@home forum: Publications on R@H's Alzheimer's work? (message 54681)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved October 8, 2008.
Baker D. "David Baker's Rosetta@home journal archives (message 40756)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved September 7, 2008.
Kim DE (2008). "Rosetta@home: Problems with minirosetta version 1.+ (Message 51199)". Rosetta@home forums. University of Washington. Archived from the original on February 26, 2009. Retrieved September 7, 2008.
"Protein–protein docking at Rosetta@home". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved September 7, 2008.
Baker D. "David Baker's Rosetta@home journal, message 52902". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved September 7, 2008.
Baker D. "David Baker's Rosetta@home journal (message 52963)". Rosetta@home forums. University of Washington. Archived from the original on June 23, 2008. Retrieved September 16, 2008.
"Rosetta@home". Archived from the original on January 3, 2016. Retrieved March 19, 2020.
"Rosetta@home: The new credit system explained". Rosetta@home forums. University of Washington. 2006. Archived from the original on February 2, 2009. Retrieved October 8, 2008.
"Rosetta@home: Predictor of the day archive". Rosetta@home. University of Washington. 2008. Archived from the original on September 24, 2008. Retrieved October 8, 2008.
"Rosetta@home: Protein Folding, Design, and Docking". Rosetta@home. University of Washington. 2008. Archived from the original on February 28, 2011. Retrieved October 8, 2008.

bakerlab.org

"De novo minibinders target SARS-CoV-2 Spike protein". Baker Lab. September 9, 2020. Archived from the original on September 30, 2020. Retrieved September 19, 2020.

robetta.bakerlab.org

"Robetta". robetta.bakerlab.org. Computing resources are provided by the Baker lab, HHMI's Janelia Research Campus, and by volunteers from the distributed computing project Rosetta@home. You can help this service by joining Rosetta@home.

ralph.bakerlab.org

"RALPH@home website". RALPH@home forums. University of Washington. Archived from the original on January 13, 2016. Retrieved September 7, 2008.

berkeley.edu (Global: 580^th place; English: 462^nd place)

boinc.berkeley.edu

"Download BOINC client software". BOINC. University of California. 2008. Archived from the original on December 7, 2008. Retrieved December 1, 2008.
"Project list – BOINC". University of California. Archived from the original on September 8, 2008. Retrieved September 8, 2008.

boincstats.com (Global: low place; English: low place)

"Rosetta@Home – Detailed stats | BOINCstats/BAM!". Archived from the original on February 11, 2019. Retrieved October 20, 2018.
"Rosetta@home: Credit overview". boincstats.com. Archived from the original on April 21, 2020. Retrieved March 28, 2020.
"BOINCstats: Project Credit Comparison". boincstats.com. 2008. Archived from the original on September 13, 2008. Retrieved October 8, 2008.
"Credit divided over projects". boincstats.com. Archived from the original on February 20, 2015. Retrieved February 19, 2015.

doi.org (Global: 2^nd place; English: 2^nd place)

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. S2CID 25383642.
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, et al. (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.
Santos, Rita; Ursu, Oleg; Gaulton, Anna; Bento, A. Patricia; Donadi, Ramesh S.; Bologna, Cristian G.; Karlsson, Anneli; Al-Lazikani, Bissan; Hersey, Anne; Oprea, Tudor I.; Overington, John P. (December 2, 2016). "A comprehensive map of molecular drug targets". Nature Reviews Drug Discovery. 16 (1): 19–34. doi:10.1038/nrd.2016.230. PMC 6314433. PMID 27910877.
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. S2CID 31575350.
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. S2CID 33172629.
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. S2CID 38430899.
Das R, Qian B, Raman S, et al. (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. S2CID 17470364.
Wang C, Schueler-Furman O, Andre I, et al. (December 2007). "RosettaDock in CAPRI rounds 6–12". Proteins. 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979. S2CID 9028237. A large amount of docking computation for the pre-dictions of target 27 and 28 was carried out on Rosetta@Home (www.boinc.bakerlab.org), a distributed comput-ing project running Rosetta software on personal com-puters of volunteers from all over the world using the Berkeley Open Infrastructure for Network Computing (BOINC) technology (www.boinc.berkeley.edu).
Jiang L, Althoff EA, Clemente FR, et al. (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.
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, et al. (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. S2CID 17672050.
Lacy DB, Lin HC, Melnyk RA, et al. (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, et al. (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, et al. (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, et al. (July 2021). "Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease". 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, et al. (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.
Walls AC, Fiala B, Schäfer A, Wrenn S, Pham MN, Murphy M, et al. (November 2020). "Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2". Cell. 183 (5): 1367–1382.e17. doi:10.1016/j.cell.2020.10.043. PMC 7604136. PMID 33160446.
Simons KT, Bonneau R, Ruczinski I, Baker D (1999). "Ab initio protein structure prediction of CASP III targets using Rosetta". Proteins. Suppl 3 (S3): 171–76. doi:10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z. PMID 10526365. S2CID 5774447.
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. S2CID 18542707.
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. S2CID 1939390.
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. S2CID 83109899.
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. S2CID 29787060.
Gray JJ, Moughon SE, Kortemme T, et al. (July 2003). "Protein–protein docking predictions for the CAPRI experiment". Proteins. 52 (1): 118–22. CiteSeerX 10.1.1.80.9354. doi:10.1002/prot.10384. PMID 12784377. S2CID 1186127.
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. CiteSeerX 10.1.1.521.9981. doi:10.1002/prot.20555. PMID 15981262. S2CID 21137936. Archived from the original on June 30, 2012.
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. S2CID 24626361. Archived from the original on June 30, 2012.
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. S2CID 22274928.
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. S2CID 24617067.
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. S2CID 29879391.
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. S2CID 8122486.
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.
Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N.; Schaeffer, R. Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R.; DeGiovanni, Andy; Pereira, Jose H.; Rodrigues, Andria V.; van Dijk, Alberdina A.; Ebrecht, Ana C.; Opperman, Diederik J.; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K.; Dalwadi, Udit; Yip, Calvin K.; Burke, John E.; Garcia, K. Christopher; Grishin, Nick V.; Adams, Paul D.; Read, Randy J.; Baker, David (August 20, 2021). "Accurate prediction of protein structures and interactions using a three-track neural network". Science. 373 (6557): 871–876. Bibcode:2021Sci...373..871B. doi:10.1126/science.abj8754. PMC 7612213. PMID 34282049.
Peng, Z; Wang, W; Han, R; Zhang, F; Yang, J (December 2022). "Protein structure prediction in the deep learning era". Current Opinion in Structural Biology. 77 102495. doi:10.1016/j.sbi.2022.102495. PMID 36371845. S2CID 253470306.
Du, Zongyang; Su, Hong; Wang, Wenkai; Ye, Lisha; Wei, Hong; Peng, Zhenling; Anishchenko, Ivan; Baker, David; Yang, Jianyi (December 2021). "The trRosetta server for fast and accurate protein structure prediction". Nature Protocols. 16 (12): 5634–5651. doi:10.1038/s41596-021-00628-9. PMID 34759384. S2CID 243987300.
Malmström L, Riffle M, Strauss CE, et al. (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.

fah-addict.net (Global: low place; English: low place)

en.fah-addict.net

jmn (July 29, 2011). "Rosetta@home and Folding@home: additional projects". Archived from the original on September 23, 2011. Retrieved September 19, 2011.

fold.it (Global: low place; English: low place)

"Foldit forums: How many users does Foldit have? Etc. (message 2)". University of Washington. Archived from the original on September 22, 2008. Retrieved September 27, 2008.
"Foldit: Frequently Asked Questions". fold.it. University of Washington. Archived from the original on September 14, 2008. Retrieved September 19, 2008.

foldingforum.org (Global: low place; English: low place)

7im (April 2, 2010). "Re: Answers to: Reasons for not using F@H". Archived from the original on August 24, 2021. Retrieved September 19, 2011.{{cite web}}: CS1 maint: numeric names: authors list (link)
tjlane (June 9, 2011). "Re: Course grained Protein folding in under 10 minutes". Archived from the original on November 11, 2012. Retrieved September 19, 2011.

gcgh.org (Global: low place; English: low place)

"Homing Endonuclease Genes: New Tools for Mosquito Population Engineering and Control". Grand Challenges in Global Health. Archived from the original on July 6, 2008. Retrieved September 7, 2008.

harvard.edu (Global: 18^th place; English: 17^th place)

ui.adsabs.harvard.edu

Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, et al. (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, et al. (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, et al. (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, et al. (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.
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. S2CID 1939390.
Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N.; Schaeffer, R. Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R.; DeGiovanni, Andy; Pereira, Jose H.; Rodrigues, Andria V.; van Dijk, Alberdina A.; Ebrecht, Ana C.; Opperman, Diederik J.; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K.; Dalwadi, Udit; Yip, Calvin K.; Burke, John E.; Garcia, K. Christopher; Grishin, Nick V.; Adams, Paul D.; Read, Randy J.; Baker, David (August 20, 2021). "Accurate prediction of protein structures and interactions using a three-track neural network". Science. 373 (6557): 871–876. Bibcode:2021Sci...373..871B. doi:10.1126/science.abj8754. PMC 7612213. PMID 34282049.

hivvaccineenterprise.org (Global: low place; English: low place)

Liu Y, et al. (2007). "Development of IgG1 b12 scaffolds and HIV-1 env-based outer domain immunogens capable of eliciting and detecting IgG1 b12-like antibodies" (PDF). Global HIV Vaccine Enterprise. Archived from the original (PDF) on February 25, 2009. Retrieved September 28, 2008.

hpcwire.com (Global: low place; English: low place)

"Rosetta@home Rallies a Legion of Computers Against the Coronavirus". HPCWire. March 24, 2020. Archived from the original on April 9, 2020. Retrieved March 25, 2020.

newyorker.com (Global: 146^th place; English: 110^th place)

Hutson M (September 18, 2020). "Scientists Advance on One of Technology's Holy Grails". The New Yorker. Archived from the original on September 18, 2020. Retrieved September 19, 2020.

nih.gov (Global: 4^th place; English: 4^th place)

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. S2CID 25383642.
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, et al. (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.
Santos, Rita; Ursu, Oleg; Gaulton, Anna; Bento, A. Patricia; Donadi, Ramesh S.; Bologna, Cristian G.; Karlsson, Anneli; Al-Lazikani, Bissan; Hersey, Anne; Oprea, Tudor I.; Overington, John P. (December 2, 2016). "A comprehensive map of molecular drug targets". Nature Reviews Drug Discovery. 16 (1): 19–34. doi:10.1038/nrd.2016.230. PMC 6314433. PMID 27910877.
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. S2CID 31575350.
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. S2CID 33172629.
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. S2CID 38430899.
Das R, Qian B, Raman S, et al. (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. S2CID 17470364.
Wang C, Schueler-Furman O, Andre I, et al. (December 2007). "RosettaDock in CAPRI rounds 6–12". Proteins. 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979. S2CID 9028237. A large amount of docking computation for the pre-dictions of target 27 and 28 was carried out on Rosetta@Home (www.boinc.bakerlab.org), a distributed comput-ing project running Rosetta software on personal com-puters of volunteers from all over the world using the Berkeley Open Infrastructure for Network Computing (BOINC) technology (www.boinc.berkeley.edu).
Jiang L, Althoff EA, Clemente FR, et al. (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, et al. (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. S2CID 17672050.
Lacy DB, Lin HC, Melnyk RA, et al. (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, et al. (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, et al. (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, et al. (July 2021). "Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease". Cell Host & Microbe. 29 (7): 1151–1161.e5. doi:10.1016/j.chom.2021.06.008. PMC 8221914. PMID 34192518.
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Walls AC, Fiala B, Schäfer A, Wrenn S, Pham MN, Murphy M, et al. (November 2020). "Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2". Cell. 183 (5): 1367–1382.e17. doi:10.1016/j.cell.2020.10.043. PMC 7604136. PMID 33160446.
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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. S2CID 18542707.
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. S2CID 1939390.
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. S2CID 83109899.
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. S2CID 29787060.
Gray JJ, Moughon SE, Kortemme T, et al. (July 2003). "Protein–protein docking predictions for the CAPRI experiment". Proteins. 52 (1): 118–22. CiteSeerX 10.1.1.80.9354. doi:10.1002/prot.10384. PMID 12784377. S2CID 1186127.
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Peng, Z; Wang, W; Han, R; Zhang, F; Yang, J (December 2022). "Protein structure prediction in the deep learning era". Current Opinion in Structural Biology. 77 102495. doi:10.1016/j.sbi.2022.102495. PMID 36371845. S2CID 253470306.
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ncbi.nlm.nih.gov

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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, et al. (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, et al. (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, et al. (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, et al. (July 2021). "Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease". 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, et al. (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.
Walls AC, Fiala B, Schäfer A, Wrenn S, Pham MN, Murphy M, et al. (November 2020). "Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2". Cell. 183 (5): 1367–1382.e17. doi:10.1016/j.cell.2020.10.043. PMC 7604136. PMID 33160446.
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.
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Malmström L, Riffle M, Strauss CE, et al. (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.

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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. S2CID 33172629.
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. S2CID 38430899.
Das R, Qian B, Raman S, et al. (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. S2CID 17470364.
Wang C, Schueler-Furman O, Andre I, et al. (December 2007). "RosettaDock in CAPRI rounds 6–12". Proteins. 69 (4): 758–63. doi:10.1002/prot.21684. PMID 17671979. S2CID 9028237. A large amount of docking computation for the pre-dictions of target 27 and 28 was carried out on Rosetta@Home (www.boinc.bakerlab.org), a distributed comput-ing project running Rosetta software on personal com-puters of volunteers from all over the world using the Berkeley Open Infrastructure for Network Computing (BOINC) technology (www.boinc.berkeley.edu).
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. S2CID 17672050.
Simons KT, Bonneau R, Ruczinski I, Baker D (1999). "Ab initio protein structure prediction of CASP III targets using Rosetta". Proteins. Suppl 3 (S3): 171–76. doi:10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z. PMID 10526365. S2CID 5774447.
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. S2CID 18542707.
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. S2CID 1939390.
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. S2CID 83109899.
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. S2CID 29787060.
Gray JJ, Moughon SE, Kortemme T, et al. (July 2003). "Protein–protein docking predictions for the CAPRI experiment". Proteins. 52 (1): 118–22. CiteSeerX 10.1.1.80.9354. doi:10.1002/prot.10384. PMID 12784377. S2CID 1186127.
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. CiteSeerX 10.1.1.521.9981. doi:10.1002/prot.20555. PMID 15981262. S2CID 21137936. Archived from the original on June 30, 2012.
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. S2CID 24626361. Archived from the original on June 30, 2012.
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. S2CID 22274928.
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. S2CID 24617067.
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. S2CID 29879391.
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worldcat.org (Global: 5^th place; English: 5^th place)

search.worldcat.org

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