Protein design (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Protein design" in English language version.

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65nih.gov

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47doi.org

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17harvard.edu

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12semanticscholar.org

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6psu.edu

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1nature.com

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core-apps.com

plan.core-apps.com

Korendovych, Ivan (March 19, 2018). "Minimalist design of peptide and protein catalysts". American Chemical Society. Retrieved March 22, 2018.

doi.org

Richardson, JS; Richardson, DC (July 1989). "The de novo design of protein structures". Trends in Biochemical Sciences. 14 (7): 304–9. doi:10.1016/0968-0004(89)90070-4. PMID 2672455.
Dahiyat, BI; Mayo, SL (October 3, 1997). "De novo protein design: fully automated sequence selection". Science. 278 (5335): 82–7. CiteSeerX 10.1.1.72.7304. doi:10.1126/science.278.5335.82. PMID 9311930.
Gordon, DB; Marshall, SA; Mayo, SL (August 1999). "Energy functions for protein design". Current Opinion in Structural Biology. 9 (4): 509–13. doi:10.1016/s0959-440x(99)80072-4. PMID 10449371.
Harbury, PB; Plecs, JJ; Tidor, B; Alber, T; Kim, PS (November 20, 1998). "High-resolution protein design with backbone freedom". Science. 282 (5393): 1462–7. doi:10.1126/science.282.5393.1462. PMID 9822371.
Kuhlman, B; Dantas, G; Ireton, GC; Varani, G; Stoddard, BL; Baker, D (November 21, 2003). "Design of a novel globular protein fold with atomic-level accuracy". Science. 302 (5649): 1364–8. Bibcode:2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033. S2CID 1939390.
Sterner, R; Merkl, R; Raushel, FM (May 2008). "Computational design of enzymes". Chemistry & Biology. 15 (5): 421–3. doi:10.1016/j.chembiol.2008.04.007. PMID 18482694.
Wu, X; Yang, ZY; Li, Y; Hogerkorp, CM; Schief, WR; Seaman, MS; Zhou, T; Schmidt, SD; Wu, L; Xu, L; Longo, NS; McKee, K; O'Dell, S; Louder, MK; Wycuff, DL; Feng, Y; Nason, M; Doria-Rose, N; Connors, M; Kwong, PD; Roederer, M; Wyatt, RT; Nabel, GJ; Mascola, JR (August 13, 2010). "Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1". Science. 329 (5993): 856–61. Bibcode:2010Sci...329..856W. doi:10.1126/science.1187659. PMC 2965066. PMID 20616233.
Höcker, B (November 8, 2012). "Structural biology: A toolbox for protein design". Nature. 491 (7423): 204–5. Bibcode:2012Natur.491..204H. doi:10.1038/491204a. PMID 23135466. S2CID 4426247.
Lovell, SC; Word, JM; Richardson, JS; Richardson, DC (August 15, 2000). "The penultimate rotamer library". Proteins. 40 (3): 389–408. CiteSeerX 10.1.1.555.4071. doi:10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2. PMID 10861930. S2CID 3055173.
Shapovalov, MV; Dunbrack RL, Jr (June 8, 2011). "A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions". Structure. 19 (6): 844–58. doi:10.1016/j.str.2011.03.019. PMC 3118414. PMID 21645855.
Samish, I; MacDermaid, CM; Perez-Aguilar, JM; Saven, JG (2011). "Theoretical and computational protein design". Annual Review of Physical Chemistry. 62: 129–49. Bibcode:2011ARPC...62..129S. doi:10.1146/annurev-physchem-032210-103509. PMID 21128762.
Mandell, DJ; Kortemme, T (August 2009). "Backbone flexibility in computational protein design" (PDF). Current Opinion in Biotechnology. 20 (4): 420–8. doi:10.1016/j.copbio.2009.07.006. PMID 19709874.
Boas, F. E. & Harbury, P. B. (2007). "Potential energy functions for protein design". Current Opinion in Structural Biology. 17 (2): 199–204. doi:10.1016/j.sbi.2007.03.006. PMID 17387014.
Boas, FE; Harbury, PB (April 2007). "Potential energy functions for protein design". Current Opinion in Structural Biology. 17 (2): 199–204. doi:10.1016/j.sbi.2007.03.006. PMID 17387014.
Vizcarra, CL; Mayo, SL (December 2005). "Electrostatics in computational protein design". Current Opinion in Chemical Biology. 9 (6): 622–6. doi:10.1016/j.cbpa.2005.10.014. PMID 16257567.
Zhou, T; Georgiev, I; Wu, X; Yang, ZY; Dai, K; Finzi, A; Kwon, YD; Scheid, JF; Shi, W; Xu, L; Yang, Y; Zhu, J; Nussenzweig, MC; Sodroski, J; Shapiro, L; Nabel, GJ; Mascola, JR; Kwong, PD (August 13, 2010). "Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01". Science. 329 (5993): 811–7. Bibcode:2010Sci...329..811Z. doi:10.1126/science.1192819. PMC 2981354. PMID 20616231.
Mendes, J; Guerois, R; Serrano, L (August 2002). "Energy estimation in protein design". Current Opinion in Structural Biology. 12 (4): 441–6. doi:10.1016/s0959-440x(02)00345-7. PMID 12163065.
Pierce, NA; Winfree, E (October 2002). "Protein design is NP-hard". Protein Engineering. 15 (10): 779–82. doi:10.1093/protein/15.10.779. PMID 12468711.
Voigt, CA; Gordon, DB; Mayo, SL (June 9, 2000). "Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design". Journal of Molecular Biology. 299 (3): 789–803. CiteSeerX 10.1.1.138.2023. doi:10.1006/jmbi.2000.3758. PMID 10835284.
Hong, EJ; Lippow, SM; Tidor, B; Lozano-Pérez, T (September 2009). "Rotamer optimization for protein design through MAP estimation and problem-size reduction". Journal of Computational Chemistry. 30 (12): 1923–45. doi:10.1002/jcc.21188. PMC 3495010. PMID 19123203.
Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020). "An evolution-based model for designing chorismatemutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. PMID 32703877. S2CID 220714458.
Wang, Jue; Lisanza, Sidney; Juergens, David; Tischer, Doug; Watson, Joseph L.; Castro, Karla M.; Ragotte, Robert; Saragovi, Amijai; Milles, Lukas F.; Baek, Minkyung; Anishchenko, Ivan; Yang, Wei; Hicks, Derrick R.; Expòsit, Marc; Schlichthaerle, Thomas; Chun, Jung-Ho; Dauparas, Justas; Bennett, Nathaniel; Wicky, Basile I. M.; Muenks, Andrew; DiMaio, Frank; Correia, Bruno; Ovchinnikov, Sergey; Baker, David (July 22, 2022). "Scaffolding protein functional sites using deep learning" (PDF). Science. 377 (6604): 387–394. Bibcode:2022Sci...377..387W. doi:10.1126/science.abn2100. ISSN 0036-8075. PMC 9621694. PMID 35862514.
Gordon, DB; Mayo, SL (September 15, 1999). "Branch-and-terminate: a combinatorial optimization algorithm for protein design". Structure. 7 (9): 1089–98. doi:10.1016/s0969-2126(99)80176-2. PMID 10508778.
Leach, AR; Lemon, AP (November 1, 1998). "Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm". Proteins. 33 (2): 227–39. CiteSeerX 10.1.1.133.7986. doi:10.1002/(sici)1097-0134(19981101)33:2<227::aid-prot7>3.0.co;2-f. PMID 9779790. S2CID 12872539.
Kingsford, CL; Chazelle, B; Singh, M (April 1, 2005). "Solving and analyzing side-chain positioning problems using linear and integer programming". Bioinformatics. 21 (7): 1028–36. doi:10.1093/bioinformatics/bti144. PMID 15546935.
Wainwright, Martin J; Tommi S. Jaakkola; Alan S. Willsky (2005). "MAP estimation via agreement on trees: message-passing and linear programming". IEEE Transactions on Information Theory. 51 (11): 3697–3717. CiteSeerX 10.1.1.71.9565. doi:10.1109/tit.2005.856938. S2CID 10007532.
Kolmogorov, Vladimir (October 28, 2006). "Convergent tree-reweighted message passing for energy minimization". IEEE Transactions on Pattern Analysis and Machine Intelligence. 28 (10): 1568–1583. doi:10.1109/TPAMI.2006.200. PMID 16986540. S2CID 8616813.
Allen, BD; Mayo, SL (July 30, 2006). "Dramatic performance enhancements for the FASTER optimization algorithm". Journal of Computational Chemistry. 27 (10): 1071–5. CiteSeerX 10.1.1.425.5418. doi:10.1002/jcc.20420. PMID 16685715. S2CID 769053.
Desmet, J; Spriet, J; Lasters, I (July 1, 2002). "Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization". Proteins. 48 (1): 31–43. doi:10.1002/prot.10131. PMID 12012335. S2CID 21524437.
Baker, D (October 2010). "An exciting but challenging road ahead for computational enzyme design". Protein Science. 19 (10): 1817–9. doi:10.1002/pro.481. PMC 2998717. PMID 20717908.
Jiang, Lin; Althoff, Eric A.; Clemente, Fernando R.; Doyle, Lindsey; Rothlisberger, Daniela; Zanghellini, Alexandre; Gallaher, Jasmine L.; Betker, Jamie L.; Tanaka, Fujie (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.
Röthlisberger, Daniela; Khersonsky, Olga; Wollacott, Andrew M.; Jiang, Lin; Dechancie, Jason; Betker, Jamie; Gallaher, Jasmine L.; Althoff, Eric A.; Zanghellini, Alexandre (2008). "Kemp elimination catalysts by computational enzyme design". Nature. 453 (7192): 190–5. Bibcode:2008Natur.453..190R. doi:10.1038/nature06879. PMID 18354394.
Siegel, JB; Zanghellini, A; Lovick, HM; Kiss, G; Lambert, AR; St Clair, JL; Gallaher, JL; Hilvert, D; Gelb, MH; Stoddard, BL; Houk, KN; Michael, FE; Baker, D (July 16, 2010). "Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction". Science. 329 (5989): 309–13. Bibcode:2010Sci...329..309S. doi:10.1126/science.1190239. PMC 3241958. PMID 20647463.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Privett, HK; Kiss, G; Lee, TM; Blomberg, R; Chica, RA; Thomas, LM; Hilvert, D; Houk, KN; Mayo, SL (March 6, 2012). "Iterative approach to computational enzyme design". Proceedings of the National Academy of Sciences of the United States of America. 109 (10): 3790–5. Bibcode:2012PNAS..109.3790P. doi:10.1073/pnas.1118082108. PMC 3309769. PMID 22357762.
Chen, CY; Georgiev, I; Anderson, AC; Donald, BR (March 10, 2009). "Computational structure-based redesign of enzyme activity". Proceedings of the National Academy of Sciences of the United States of America. 106 (10): 3764–9. Bibcode:2009PNAS..106.3764C. doi:10.1073/pnas.0900266106. PMC 2645347. PMID 19228942.
Korendovych, Ivan V. (2018). "Rational and Semirational Protein Design". Protein Engineering. Methods in Molecular Biology (Clifton, N.J.). Vol. 1685. pp. 15–23. doi:10.1007/978-1-4939-7366-8_2. ISBN 978-1-4939-7364-4. ISSN 1064-3745. PMC 5912912. PMID 29086301.
Karanicolas, J; Kuhlman, B (August 2009). "Computational design of affinity and specificity at protein–protein interfaces". Current Opinion in Structural Biology. 19 (4): 458–63. doi:10.1016/j.sbi.2009.07.005. PMC 2882636. PMID 19646858.
Shoichet, BK (October 2007). "No free energy lunch". Nature Biotechnology. 25 (10): 1109–10. doi:10.1038/nbt1007-1109. PMID 17921992. S2CID 5527226.
Lippow, SM; Wittrup, KD; Tidor, B (October 2007). "Computational design of antibody-affinity improvement beyond in vivo maturation". Nature Biotechnology. 25 (10): 1171–6. doi:10.1038/nbt1336. PMC 2803018. PMID 17891135.
Schreiber, G; Keating, AE (February 2011). "Protein binding specificity versus promiscuity". Current Opinion in Structural Biology. 21 (1): 50–61. doi:10.1016/j.sbi.2010.10.002. PMC 3053118. PMID 21071205.
Grigoryan, G; Reinke, AW; Keating, AE (April 16, 2009). "Design of protein-interaction specificity gives selective bZIP-binding peptides". Nature. 458 (7240): 859–64. Bibcode:2009Natur.458..859G. doi:10.1038/nature07885. PMC 2748673. PMID 19370028.
Frey, KM; Georgiev, I; Donald, BR; Anderson, AC (August 3, 2010). "Predicting resistance mutations using protein design algorithms". Proceedings of the National Academy of Sciences of the United States of America. 107 (31): 13707–12. Bibcode:2010PNAS..10713707F. doi:10.1073/pnas.1002162107. PMC 2922245. PMID 20643959.
Khoury, GA; Fazelinia, H; Chin, JW; Pantazes, RJ; Cirino, PC; Maranas, CD (October 2009). "Computational design of Candida boidinii xylose reductase for altered cofactor specificity". Protein Science. 18 (10): 2125–38. doi:10.1002/pro.227. PMC 2786976. PMID 19693930.
Burton, DR; Weiss, RA (August 13, 2010). "AIDS/HIV. A boost for HIV vaccine design". Science. 329 (5993): 770–3. Bibcode:2010Sci...329..770B. doi:10.1126/science.1194693. PMID 20705840. S2CID 206528638.
Chowdhury, Ratul; Kumar, Manish; Maranas, Costas D.; Golbeck, John H.; Baker, Carol; Prabhakar, Jeevan; Grisewood, Matthew; Decker, Karl; Shankla, Manish (September 10, 2018). "PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore". Nature Communications. 9 (1): 3661. Bibcode:2018NatCo...9.3661C. doi:10.1038/s41467-018-06097-1. ISSN 2041-1723. PMC 6131167. PMID 30202038.
Looger, Loren L.; Dwyer, Mary A.; Smith, James J. & Hellinga, Homme W. (2003). "Computational design of receptor and sensor proteins with novel functions". Nature. 423 (6936): 185–190. Bibcode:2003Natur.423..185L. doi:10.1038/nature01556. PMID 12736688. S2CID 4387641.
Jha, RK; Wu, YI; Zawistowski, JS; MacNevin, C; Hahn, KM; Kuhlman, B (October 21, 2011). "Redesign of the PAK1 autoinhibitory domain for enhanced stability and affinity in biosensor applications". Journal of Molecular Biology. 413 (2): 513–22. doi:10.1016/j.jmb.2011.08.022. PMC 3202338. PMID 21888918.

escholarship.org

Mandell, DJ; Kortemme, T (August 2009). "Backbone flexibility in computational protein design" (PDF). Current Opinion in Biotechnology. 20 (4): 420–8. doi:10.1016/j.copbio.2009.07.006. PMID 19709874.

harvard.edu

ui.adsabs.harvard.edu

Kuhlman, B; Dantas, G; Ireton, GC; Varani, G; Stoddard, BL; Baker, D (November 21, 2003). "Design of a novel globular protein fold with atomic-level accuracy". Science. 302 (5649): 1364–8. Bibcode:2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033. S2CID 1939390.
Wu, X; Yang, ZY; Li, Y; Hogerkorp, CM; Schief, WR; Seaman, MS; Zhou, T; Schmidt, SD; Wu, L; Xu, L; Longo, NS; McKee, K; O'Dell, S; Louder, MK; Wycuff, DL; Feng, Y; Nason, M; Doria-Rose, N; Connors, M; Kwong, PD; Roederer, M; Wyatt, RT; Nabel, GJ; Mascola, JR (August 13, 2010). "Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1". Science. 329 (5993): 856–61. Bibcode:2010Sci...329..856W. doi:10.1126/science.1187659. PMC 2965066. PMID 20616233.
Höcker, B (November 8, 2012). "Structural biology: A toolbox for protein design". Nature. 491 (7423): 204–5. Bibcode:2012Natur.491..204H. doi:10.1038/491204a. PMID 23135466. S2CID 4426247.
Samish, I; MacDermaid, CM; Perez-Aguilar, JM; Saven, JG (2011). "Theoretical and computational protein design". Annual Review of Physical Chemistry. 62: 129–49. Bibcode:2011ARPC...62..129S. doi:10.1146/annurev-physchem-032210-103509. PMID 21128762.
Zhou, T; Georgiev, I; Wu, X; Yang, ZY; Dai, K; Finzi, A; Kwon, YD; Scheid, JF; Shi, W; Xu, L; Yang, Y; Zhu, J; Nussenzweig, MC; Sodroski, J; Shapiro, L; Nabel, GJ; Mascola, JR; Kwong, PD (August 13, 2010). "Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01". Science. 329 (5993): 811–7. Bibcode:2010Sci...329..811Z. doi:10.1126/science.1192819. PMC 2981354. PMID 20616231.
Russ, William P.; Figliuzzi, Matteo; Stocker, Christian; Barrat-Charlaix, Pierre; Socolich, Michael; Kast, Peter; Hilvert, Donald; Monasson, Remi; Cocco, Simona; Weigt, Martin; Ranganathan, Rama (2020). "An evolution-based model for designing chorismatemutase enzymes". Science. 369 (6502): 440–445. Bibcode:2020Sci...369..440R. doi:10.1126/science.aba3304. PMID 32703877. S2CID 220714458.
Wang, Jue; Lisanza, Sidney; Juergens, David; Tischer, Doug; Watson, Joseph L.; Castro, Karla M.; Ragotte, Robert; Saragovi, Amijai; Milles, Lukas F.; Baek, Minkyung; Anishchenko, Ivan; Yang, Wei; Hicks, Derrick R.; Expòsit, Marc; Schlichthaerle, Thomas; Chun, Jung-Ho; Dauparas, Justas; Bennett, Nathaniel; Wicky, Basile I. M.; Muenks, Andrew; DiMaio, Frank; Correia, Bruno; Ovchinnikov, Sergey; Baker, David (July 22, 2022). "Scaffolding protein functional sites using deep learning" (PDF). Science. 377 (6604): 387–394. Bibcode:2022Sci...377..387W. doi:10.1126/science.abn2100. ISSN 0036-8075. PMC 9621694. PMID 35862514.
Jiang, Lin; Althoff, Eric A.; Clemente, Fernando R.; Doyle, Lindsey; Rothlisberger, Daniela; Zanghellini, Alexandre; Gallaher, Jasmine L.; Betker, Jamie L.; Tanaka, Fujie (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.
Röthlisberger, Daniela; Khersonsky, Olga; Wollacott, Andrew M.; Jiang, Lin; Dechancie, Jason; Betker, Jamie; Gallaher, Jasmine L.; Althoff, Eric A.; Zanghellini, Alexandre (2008). "Kemp elimination catalysts by computational enzyme design". Nature. 453 (7192): 190–5. Bibcode:2008Natur.453..190R. doi:10.1038/nature06879. PMID 18354394.
Siegel, JB; Zanghellini, A; Lovick, HM; Kiss, G; Lambert, AR; St Clair, JL; Gallaher, JL; Hilvert, D; Gelb, MH; Stoddard, BL; Houk, KN; Michael, FE; Baker, D (July 16, 2010). "Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction". Science. 329 (5989): 309–13. Bibcode:2010Sci...329..309S. doi:10.1126/science.1190239. PMC 3241958. PMID 20647463.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Privett, HK; Kiss, G; Lee, TM; Blomberg, R; Chica, RA; Thomas, LM; Hilvert, D; Houk, KN; Mayo, SL (March 6, 2012). "Iterative approach to computational enzyme design". Proceedings of the National Academy of Sciences of the United States of America. 109 (10): 3790–5. Bibcode:2012PNAS..109.3790P. doi:10.1073/pnas.1118082108. PMC 3309769. PMID 22357762.
Chen, CY; Georgiev, I; Anderson, AC; Donald, BR (March 10, 2009). "Computational structure-based redesign of enzyme activity". Proceedings of the National Academy of Sciences of the United States of America. 106 (10): 3764–9. Bibcode:2009PNAS..106.3764C. doi:10.1073/pnas.0900266106. PMC 2645347. PMID 19228942.
Grigoryan, G; Reinke, AW; Keating, AE (April 16, 2009). "Design of protein-interaction specificity gives selective bZIP-binding peptides". Nature. 458 (7240): 859–64. Bibcode:2009Natur.458..859G. doi:10.1038/nature07885. PMC 2748673. PMID 19370028.
Frey, KM; Georgiev, I; Donald, BR; Anderson, AC (August 3, 2010). "Predicting resistance mutations using protein design algorithms". Proceedings of the National Academy of Sciences of the United States of America. 107 (31): 13707–12. Bibcode:2010PNAS..10713707F. doi:10.1073/pnas.1002162107. PMC 2922245. PMID 20643959.
Burton, DR; Weiss, RA (August 13, 2010). "AIDS/HIV. A boost for HIV vaccine design". Science. 329 (5993): 770–3. Bibcode:2010Sci...329..770B. doi:10.1126/science.1194693. PMID 20705840. S2CID 206528638.
Chowdhury, Ratul; Kumar, Manish; Maranas, Costas D.; Golbeck, John H.; Baker, Carol; Prabhakar, Jeevan; Grisewood, Matthew; Decker, Karl; Shankla, Manish (September 10, 2018). "PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore". Nature Communications. 9 (1): 3661. Bibcode:2018NatCo...9.3661C. doi:10.1038/s41467-018-06097-1. ISSN 2041-1723. PMC 6131167. PMID 30202038.
Looger, Loren L.; Dwyer, Mary A.; Smith, James J. & Hellinga, Homme W. (2003). "Computational design of receptor and sensor proteins with novel functions". Nature. 423 (6936): 185–190. Bibcode:2003Natur.423..185L. doi:10.1038/nature01556. PMID 12736688. S2CID 4387641.

medicalxpress.com

"Biologists train AI to generate medicines and vaccines". University of Washington-Harborview Medical Center.

nature.com

Jessica Marshall (November 7, 2012). "Proteins made to order". Nature News. Retrieved November 17, 2012.

nih.gov

pubmed.ncbi.nlm.nih.gov

Richardson, JS; Richardson, DC (July 1989). "The de novo design of protein structures". Trends in Biochemical Sciences. 14 (7): 304–9. doi:10.1016/0968-0004(89)90070-4. PMID 2672455.
Dahiyat, BI; Mayo, SL (October 3, 1997). "De novo protein design: fully automated sequence selection". Science. 278 (5335): 82–7. CiteSeerX 10.1.1.72.7304. doi:10.1126/science.278.5335.82. PMID 9311930.
Gordon, DB; Marshall, SA; Mayo, SL (August 1999). "Energy functions for protein design". Current Opinion in Structural Biology. 9 (4): 509–13. doi:10.1016/s0959-440x(99)80072-4. PMID 10449371.
Harbury, PB; Plecs, JJ; Tidor, B; Alber, T; Kim, PS (November 20, 1998). "High-resolution protein design with backbone freedom". Science. 282 (5393): 1462–7. doi:10.1126/science.282.5393.1462. PMID 9822371.
Kuhlman, B; Dantas, G; Ireton, GC; Varani, G; Stoddard, BL; Baker, D (November 21, 2003). "Design of a novel globular protein fold with atomic-level accuracy". Science. 302 (5649): 1364–8. Bibcode:2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033. S2CID 1939390.
Sterner, R; Merkl, R; Raushel, FM (May 2008). "Computational design of enzymes". Chemistry & Biology. 15 (5): 421–3. doi:10.1016/j.chembiol.2008.04.007. PMID 18482694.
Wu, X; Yang, ZY; Li, Y; Hogerkorp, CM; Schief, WR; Seaman, MS; Zhou, T; Schmidt, SD; Wu, L; Xu, L; Longo, NS; McKee, K; O'Dell, S; Louder, MK; Wycuff, DL; Feng, Y; Nason, M; Doria-Rose, N; Connors, M; Kwong, PD; Roederer, M; Wyatt, RT; Nabel, GJ; Mascola, JR (August 13, 2010). "Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1". Science. 329 (5993): 856–61. Bibcode:2010Sci...329..856W. doi:10.1126/science.1187659. PMC 2965066. PMID 20616233.
Höcker, B (November 8, 2012). "Structural biology: A toolbox for protein design". Nature. 491 (7423): 204–5. Bibcode:2012Natur.491..204H. doi:10.1038/491204a. PMID 23135466. S2CID 4426247.
Lovell, SC; Word, JM; Richardson, JS; Richardson, DC (August 15, 2000). "The penultimate rotamer library". Proteins. 40 (3): 389–408. CiteSeerX 10.1.1.555.4071. doi:10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2. PMID 10861930. S2CID 3055173.
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Samish, I; MacDermaid, CM; Perez-Aguilar, JM; Saven, JG (2011). "Theoretical and computational protein design". Annual Review of Physical Chemistry. 62: 129–49. Bibcode:2011ARPC...62..129S. doi:10.1146/annurev-physchem-032210-103509. PMID 21128762.
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Wang, Jue; Lisanza, Sidney; Juergens, David; Tischer, Doug; Watson, Joseph L.; Castro, Karla M.; Ragotte, Robert; Saragovi, Amijai; Milles, Lukas F.; Baek, Minkyung; Anishchenko, Ivan; Yang, Wei; Hicks, Derrick R.; Expòsit, Marc; Schlichthaerle, Thomas; Chun, Jung-Ho; Dauparas, Justas; Bennett, Nathaniel; Wicky, Basile I. M.; Muenks, Andrew; DiMaio, Frank; Correia, Bruno; Ovchinnikov, Sergey; Baker, David (July 22, 2022). "Scaffolding protein functional sites using deep learning" (PDF). Science. 377 (6604): 387–394. Bibcode:2022Sci...377..387W. doi:10.1126/science.abn2100. ISSN 0036-8075. PMC 9621694. PMID 35862514.
Korendovych, Ivan V. (2018). "Rational and Semirational Protein Design". Protein Engineering. Methods in Molecular Biology (Clifton, N.J.). Vol. 1685. pp. 15–23. doi:10.1007/978-1-4939-7366-8_2. ISBN 978-1-4939-7364-4. ISSN 1064-3745. PMC 5912912. PMID 29086301.
Chowdhury, Ratul; Kumar, Manish; Maranas, Costas D.; Golbeck, John H.; Baker, Carol; Prabhakar, Jeevan; Grisewood, Matthew; Decker, Karl; Shankla, Manish (September 10, 2018). "PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore". Nature Communications. 9 (1): 3661. Bibcode:2018NatCo...9.3661C. doi:10.1038/s41467-018-06097-1. ISSN 2041-1723. PMC 6131167. PMID 30202038.