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Shoehei Koide - Publications

Affiliations: 
University of Rochester, Rochester, NY 
Area:
General Biophysics
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24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ludwicki MB, Li J, Stephens EA, Roberts RW, Koide S, Hammond PT, DeLisa MP. Broad-Spectrum Proteome Editing with an Engineered Bacterial Ubiquitin Ligase Mimic. Acs Central Science. 5: 852-866. PMID 31139721 DOI: 10.1021/Acscentsci.9B00127  0.35
2019 Kawano K, Koide S, Imamura C. Seq2seq Fingerprint with Byte-Pair Encoding for Predicting Changes in Protein Stability upon Single Point Mutation. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30946675 DOI: 10.1109/TCBB.2019.2908641  0.382
2018 Makabe K, Nakamura T, Dhar D, Ikura T, Koide S, Kuwajima K. An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior. Journal of Molecular Biology. PMID 29709572 DOI: 10.1016/J.Jmb.2018.04.025  0.326
2017 Sha F, Salzman G, Gupta A, Koide S. Monobodies and Other Synthetic Binding Proteins for Expanding Protein Science. Protein Science : a Publication of the Protein Society. PMID 28249355 DOI: 10.1002/Pro.3148  0.345
2013 Paduch M, Koide A, Uysal S, Rizk SS, Koide S, Kossiakoff AA. Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods (San Diego, Calif.). 60: 3-14. PMID 23280336 DOI: 10.1016/J.Ymeth.2012.12.010  0.337
2012 Koide S, Koide A, Lipovšek D. Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3). Methods in Enzymology. 503: 135-56. PMID 22230568 DOI: 10.1016/B978-0-12-396962-0.00006-9  0.388
2012 Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S. Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. Journal of Molecular Biology. 415: 393-405. PMID 22198408 DOI: 10.1016/J.Jmb.2011.12.019  0.32
2009 Koide A, Wojcik J, Gilbreth RN, Reichel A, Piehler J, Koide S. Accelerating phage-display library selection by reversible and site-specific biotinylation. Protein Engineering, Design & Selection : Peds. 22: 685-90. PMID 19737805 DOI: 10.1093/Protein/Gzp053  0.335
2009 Koide S. Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. Current Opinion in Biotechnology. 20: 398-404. PMID 19700302 DOI: 10.1016/J.Copbio.2009.07.007  0.305
2009 Huang J, Makabe K, Biancalana M, Koide A, Koide S. Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. Journal of Molecular Biology. 392: 1221-31. PMID 19646997 DOI: 10.1016/J.Jmb.2009.07.067  0.301
2009 Koide S, Sidhu SS. The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. Acs Chemical Biology. 4: 325-34. PMID 19298050 DOI: 10.1021/Cb800314V  0.347
2008 Dutta S, Koide A, Koide S. High-throughput analysis of the protein sequence-stability landscape using a quantitative yeast surface two-hybrid system and fragment reconstitution. Journal of Molecular Biology. 382: 721-33. PMID 18674545 DOI: 10.1016/J.Jmb.2008.07.036  0.552
2008 Kossiakoff AA, Koide S. Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces. Current Opinion in Structural Biology. 18: 499-506. PMID 18638552 DOI: 10.1016/J.Sbi.2008.06.004  0.34
2008 Gilbreth RN, Esaki K, Koide A, Sidhu SS, Koide S. A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. Journal of Molecular Biology. 381: 407-18. PMID 18602117 DOI: 10.1016/J.Jmb.2008.06.014  0.307
2008 Huang J, Koide A, Makabe K, Koide S. Design of protein function leaps by directed domain interface evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 6578-83. PMID 18445649 DOI: 10.1073/Pnas.0801097105  0.307
2007 Koide A, Tereshko V, Uysal S, Margalef K, Kossiakoff AA, Koide S. Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. Journal of Molecular Biology. 373: 941-53. PMID 17888451 DOI: 10.1016/J.Jmb.2007.08.027  0.317
2007 Sidhu SS, Koide S. Phage display for engineering and analyzing protein interaction interfaces. Current Opinion in Structural Biology. 17: 481-7. PMID 17870470 DOI: 10.1016/J.Sbi.2007.08.007  0.354
2007 Koide A, Gilbreth RN, Esaki K, Tereshko V, Koide S. High-affinity single-domain binding proteins with a binary-code interface. Proceedings of the National Academy of Sciences of the United States of America. 104: 6632-7. PMID 17420456 DOI: 10.1073/Pnas.0700149104  0.36
2007 Koide A, Koide S. Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. Methods in Molecular Biology (Clifton, N.J.). 352: 95-109. PMID 17041261 DOI: 10.1385/1-59745-187-8:95  0.37
2005 Dutta S, Batori V, Koide A, Koide S. High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement. Protein Science : a Publication of the Protein Society. 14: 2838-48. PMID 16199661 DOI: 10.1110/Ps.051603005  0.554
2004 Murphy WL, Mercurius KO, Koide S, Mrksich M. Substrates for Cell Adhesion Prepared via Active Site-Directed Immobilization of a Protein Domain Langmuir. 20: 1026-1030. PMID 15803670 DOI: 10.1021/La035733M  0.332
2003 Richards J, Miller M, Abend J, Koide A, Koide S, Dewhurst S. Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin. Journal of Molecular Biology. 326: 1475-88. PMID 12595259 DOI: 10.1016/S0022-2836(03)00082-2  0.343
2002 Batori V, Koide A, Koide S. Exploring the potential of the monobody scaffold: effects of loop elongation on the stability of a fibronectin type III domain. Protein Engineering. 15: 1015-20. PMID 12601141 DOI: 10.1093/Protein/15.12.1015  0.373
1998 Koide A, Bailey CW, Huang X, Koide S. The fibronectin type III domain as a scaffold for novel binding proteins Journal of Molecular Biology. 284: 1141-1151. PMID 9837732 DOI: 10.1006/Jmbi.1998.2238  0.43
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