| Year |
Citation |
Score |
| 2023 |
Koide A, Koide S. Use of Phage Display and Other Molecular Display Methods for the Development of Monobodies. Cold Spring Harbor Protocols. PMID 37137569 DOI: 10.1101/pdb.over107982 |
0.405 |
|
| 2023 |
Sha F, Kurosawa K, Glasser E, Ketavarapu G, Albazzaz S, Koide A, Koide S. Monobody inhibitor selective to the phosphatase domain of SHP2 and its use as a probe for quantifying SHP2 allosteric regulation. Journal of Molecular Biology. 168010. PMID 36806475 DOI: 10.1016/j.jmb.2023.168010 |
0.359 |
|
| 2021 |
Garnish SE, Meng Y, Koide A, Sandow JJ, Denbaum E, Jacobsen AV, Yeung W, Samson AL, Horne CR, Fitzgibbon C, Young SN, Smith PPC, Webb AI, Petrie EJ, Hildebrand JM, ... ... Koide S, et al. Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis. Nature Communications. 12: 2211. PMID 33850121 DOI: 10.1038/s41467-021-22400-z |
0.358 |
|
| 2020 |
Hattori T, Koide A, Noval MG, Panchenko T, Romero LA, Wen Teng K, Tada T, Landau NR, Stapleford KA, Koide S. The ACE2-binding interface of SARS-CoV-2 Spike inherently deflects immune recognition. Journal of Molecular Biology. 166748. PMID 33310017 DOI: 10.1016/j.jmb.2020.166748 |
0.313 |
|
| 2020 |
Hattori T, Koide A, Panchenko T, Romero LA, Teng KW, Tada T, Landau NR, Koide S. The ACE2-binding interface of SARS-CoV-2 Spike inherently deflects immune recognition. Biorxiv : the Preprint Server For Biology. PMID 33173869 DOI: 10.1101/2020.11.03.365270 |
0.312 |
|
| 2020 |
Salzman GS, Zhang S, Fernandez CG, Araç D, Koide S. Specific and direct modulation of the interaction between adhesion GPCR GPR56/ADGRG1 and tissue transglutaminase 2 using synthetic ligands. Scientific Reports. 10: 16912. PMID 33037308 DOI: 10.1038/s41598-020-74044-6 |
0.326 |
|
| 2020 |
Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Structural basis for the reaction cycle of DASS dicarboxylate transporters. Elife. 9. PMID 32869741 DOI: 10.7554/Elife.61350 |
0.319 |
|
| 2020 |
La Sala G, Michiels C, Kükenshöner T, Brandstoetter T, Maurer B, Koide A, Lau K, Pojer F, Koide S, Sexl V, Dumoutier L, Hantschel O. Selective inhibition of STAT3 signaling using monobodies targeting the coiled-coil and N-terminal domains. Nature Communications. 11: 4115. PMID 32807795 DOI: 10.1038/S41467-020-17920-Z |
0.422 |
|
| 2020 |
Petrie EJ, Birkinshaw RW, Koide A, Denbaum E, Hildebrand JM, Garnish SE, Davies KA, Sandow JJ, Samson AL, Gavin X, Fitzgibbon C, Young SN, Hennessy PJ, Smith PPC, Webb AI, ... ... Koide S, et al. Identification of MLKL membrane translocation as a checkpoint in necroptotic cell death using Monobodies. Proceedings of the National Academy of Sciences of the United States of America. PMID 32234780 DOI: 10.1073/Pnas.1919960117 |
0.432 |
|
| 2020 |
Lee KY, Fang Z, Enomoto M, Seabrook GG, Zheng L, Koide S, Ikura M, Marshall CB. Two Distinct Structures of Membrane-associated Homodimers of GTP- and GDP-bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. Angewandte Chemie (International Ed. in English). PMID 32227412 DOI: 10.1002/Anie.202001758 |
0.375 |
|
| 2020 |
Hantschel O, Biancalana M, Koide S. Monobodies as enabling tools for structural and mechanistic biology. Current Opinion in Structural Biology. 60: 167-174. PMID 32145686 DOI: 10.1016/J.Sbi.2020.01.015 |
0.421 |
|
| 2019 |
Röck R, Mayrhofer JE, Torres-Quesada O, Enzler F, Raffeiner A, Raffeiner P, Feichtner A, Huber RG, Koide S, Taylor SS, Troppmair J, Stefan E. BRAF inhibitors promote intermediate BRAF(V600E) conformations and binary interactions with activated RAS. Science Advances. 5: eaav8463. PMID 31453322 DOI: 10.1126/Sciadv.Aav8463 |
0.329 |
|
| 2019 |
Koide S. Repurposing off-the-shelf antihelix antibodies for enabling structural biology. Proceedings of the National Academy of Sciences of the United States of America. PMID 31427527 DOI: 10.1073/Pnas.1912643116 |
0.415 |
|
| 2019 |
Zorba A, Nguyen V, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S, Kern D. Allosteric modulation of a human protein kinase with monobodies. Proceedings of the National Academy of Sciences of the United States of America. PMID 31239342 DOI: 10.1073/Pnas.1906024116 |
0.414 |
|
| 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 |
0.424 |
|
| 2019 |
Chen L, Wang W, Koide A, Bolen J, Miller G, Koide S. Abstract 1551: First in class immunotherapy targeting Galectin-9 promotes T-cell activation and anti-tumor response against pancreatic cancer and other solid tumors Cancer Research. 79: 1551-1551. DOI: 10.1158/1538-7445.Am2019-1551 |
0.314 |
|
| 2018 |
Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nature Chemical Biology. PMID 30013062 DOI: 10.1038/S41589-018-0099-Z |
0.382 |
|
| 2018 |
Tanaka SI, Takahashi T, Koide A, Iwamoto R, Koikeda S, Koide S. Monobody-mediated alteration of lipase substrate specificity. Acs Chemical Biology. PMID 29757606 DOI: 10.1021/Acschembio.8B00384 |
0.329 |
|
| 2018 |
Hattori T, Koide S. Next-generation antibodies for post-translational modifications. Current Opinion in Structural Biology. 51: 141-148. PMID 29753204 DOI: 10.1016/J.Sbi.2018.04.006 |
0.383 |
|
| 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 |
0.404 |
|
| 2017 |
Reckel S, Gehin C, Tardivon D, Georgeon S, Kükenshöner T, Löhr F, Koide A, Buchner L, Panjkovich A, Reynaud A, Pinho S, Gerig B, Svergun D, Pojer F, Güntert P, ... ... Koide S, et al. Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase. Nature Communications. 8: 2101. PMID 29235475 DOI: 10.1038/S41467-017-02313-6 |
0.349 |
|
| 2017 |
Ghosh E, Srivastava A, Baidya M, Kumari P, Dwivedi H, Nidhi K, Ranjan R, Dogra S, Koide A, Yadav PN, Sidhu SS, Koide S, Shukla AK. A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis. Nature Nanotechnology. PMID 28967893 DOI: 10.1038/Nnano.2017.188 |
0.392 |
|
| 2017 |
Salzman GS, Zhang S, Gupta A, Koide A, Koide S, Araç D. Stachel-independent modulation of GPR56/ADGRG1 signaling by synthetic ligands directed to its extracellular region. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874577 DOI: 10.1073/Pnas.1708810114 |
0.351 |
|
| 2017 |
Rizk SS, Mukherjee S, Koide A, Koide S, Kossiakoff AA. Targeted rescue of cancer-associated IDH1 mutant activity using an engineered synthetic antibody. Scientific Reports. 7: 556. PMID 28373671 DOI: 10.1038/S41598-017-00728-1 |
0.343 |
|
| 2017 |
Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, Seeliger M, Koide S, Hantschel O. Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. Journal of Molecular Biology. PMID 28347651 DOI: 10.1016/J.Jmb.2017.03.023 |
0.46 |
|
| 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 |
0.473 |
|
| 2017 |
Bowman A, Koide A, Goodman JS, Colling ME, Zinne D, Koide S, Ladurner AG. sNASP and ASF1A function through both competitive and compatible modes of histone binding. Nucleic Acids Research. 45: 643-656. PMID 28123037 DOI: 10.1093/Nar/Gkw892 |
0.327 |
|
| 2016 |
Sachleben JR, Adhikari AN, Gawlak G, Hoey RJ, Liu G, Joachimiak A, Montelione GT, Sosnick TR, Koide S. Aromatic Claw: A new fold with high aromatic content that evades structural prediction. Protein Science : a Publication of the Protein Society. PMID 27750371 DOI: 10.1002/Pro.3069 |
0.348 |
|
| 2016 |
Salzman GS, Ackerman SD, Ding C, Koide A, Leon K, Luo R, Stoveken HM, Fernandez CG, Tall GG, Piao X, Monk KR, Koide S, Araç D. Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains. Neuron. 91: 1292-1304. PMID 27657451 DOI: 10.1016/J.Neuron.2016.08.022 |
0.375 |
|
| 2016 |
Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA. Specific Recognition of a Single-stranded RNA Sequence by a Synthetic Antibody Fragment. Journal of Molecular Biology. PMID 27593161 DOI: 10.1016/J.Jmb.2016.08.029 |
0.32 |
|
| 2016 |
Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, Hantschel O, Koide S. Allosteric Inhibition of Bcr-Abl Kinase by High-Affinity Monobody Inhibitors Directed to the SH2-Kinase Interface. The Journal of Biological Chemistry. PMID 26912659 DOI: 10.1074/Jbc.M115.707901 |
0.732 |
|
| 2016 |
Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26862167 DOI: 10.1073/Pnas.1522691113 |
0.381 |
|
| 2016 |
Hantschel O, Reckel S, Romain H, Armand F, Harduin D, Koide S, Dötsch V, Moniatte M. Comprehensive Analysis of the Structural, Biochemical and Signaling Differences of the p210 and p185 Isoforms of Bcr-Abl in CML and B-ALL Blood. 128: 4238-4238. DOI: 10.1182/Blood.V128.22.4238.4238 |
0.327 |
|
| 2015 |
Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J. ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. Elife. 4. PMID 26523391 DOI: 10.7554/Elife.10150 |
0.4 |
|
| 2015 |
Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, et al. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. Plos One. 10: e0139695. PMID 26437229 DOI: 10.1371/Journal.Pone.0139695 |
0.361 |
|
| 2015 |
Tanaka S, Takahashi T, Koide A, Ishihara S, Koikeda S, Koide S. Monobody-mediated alteration of enzyme specificity. Nature Chemical Biology. 11: 762-4. PMID 26322825 DOI: 10.1038/Nchembio.1896 |
0.312 |
|
| 2015 |
Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, ... ... Koide S, et al. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Molecular & Cellular Proteomics : McP. PMID 26290498 DOI: 10.1074/Mcp.O115.052209 |
0.397 |
|
| 2015 |
Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, ... ... Koide S, et al. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nature Methods. PMID 26121405 DOI: 10.1038/Nmeth.3472 |
0.36 |
|
| 2015 |
Miersch S, Li Z, Hanna R, McLaughlin ME, Hornsby M, Matsuguchi T, Paduch M, Sääf A, Wells J, Koide S, Kossiakoff A, Sidhu SS. Scalable high throughput selection from phage-displayed synthetic antibody libraries. Journal of Visualized Experiments : Jove. 51492. PMID 25651360 DOI: 10.3791/51492 |
0.377 |
|
| 2015 |
Biancalana M, Makabe K, Yan S, Koide S. Aromatic cluster mutations produce focal modulations of β-sheet structure. Protein Science : a Publication of the Protein Society. 24: 841-9. PMID 25645104 DOI: 10.1002/Pro.2657 |
0.332 |
|
| 2015 |
Griffin C, Miersch S, Marcon E, Banerjee S, Wells J, Hornsby M, Kossiakoff A, Koide S, Paduch M, Sidhu S, Moffat J. Validation of Recombinant Antibodies Against Human Transcription Factors The Faseb Journal. 29. DOI: 10.1096/Fasebj.29.1_Supplement.571.13 |
0.313 |
|
| 2015 |
Stockbridge R, Kolmakova-Partensky L, Koide A, Koide S, Newstead S, Miller C. Crystal Structure of Fluc, a Microbial Fluoride Channel Biophysical Journal. 108: 440a. DOI: 10.1016/J.Bpj.2014.11.2405 |
0.339 |
|
| 2014 |
Zhang X, Hoey R, Koide A, Dolios G, Paduch M, Nguyen P, Wu X, Li Y, Wagner SL, Wang R, Koide S, Sisodia SS. A synthetic antibody fragment targeting nicastrin affects assembly and trafficking of γ-secretase. The Journal of Biological Chemistry. 289: 34851-61. PMID 25352592 DOI: 10.1074/Jbc.M114.609636 |
0.361 |
|
| 2014 |
Stockbridge RB, Koide A, Miller C, Koide S. Proof of dual-topology architecture of Fluc F- channels with monobody blockers. Nature Communications. 5: 5120. PMID 25290819 DOI: 10.1038/Ncomms6120 |
0.33 |
|
| 2014 |
Jose CC, Xu B, Jagannathan L, Trac C, Mallela RK, Hattori T, Lai D, Koide S, Schones DE, Cuddapah S. Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proceedings of the National Academy of Sciences of the United States of America. 111: 14631-6. PMID 25246589 DOI: 10.1073/Pnas.1406923111 |
0.35 |
|
| 2014 |
Shukla AK, Westfield GH, Xiao K, Reis RI, Huang LY, Tripathi-Shukla P, Qian J, Li S, Blanc A, Oleskie AN, Dosey AM, Su M, Liang CR, Gu LL, Shan JM, ... ... Koide S, et al. Visualization of arrestin recruitment by a G-protein-coupled receptor. Nature. 512: 218-22. PMID 25043026 DOI: 10.1038/Nature13430 |
0.334 |
|
| 2014 |
Yasui N, Findlay GM, Gish GD, Hsiung MS, Huang J, Tucholska M, Taylor L, Smith L, Boldridge WC, Koide A, Pawson T, Koide S. Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation. Molecular Cell. 54: 1034-41. PMID 24910098 DOI: 10.1016/J.Molcel.2014.05.002 |
0.389 |
|
| 2013 |
Sha F, Gencer EB, Georgeon S, Koide A, Yasui N, Koide S, Hantschel O. Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proceedings of the National Academy of Sciences of the United States of America. 110: 14924-9. PMID 23980151 DOI: 10.1073/Pnas.1303640110 |
0.474 |
|
| 2013 |
McCord LA, Liang WG, Dowdell E, Kalas V, Hoey RJ, Koide A, Koide S, Tang WJ. Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme. Proceedings of the National Academy of Sciences of the United States of America. 110: 13827-32. PMID 23922390 DOI: 10.1073/Pnas.1304575110 |
0.315 |
|
| 2013 |
Shukla AK, Manglik A, Kruse AC, Xiao K, Reis RI, Tseng WC, Staus DP, Hilger D, Uysal S, Huang LY, Paduch M, Tripathi-Shukla P, Koide A, Koide S, Weis WI, et al. Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide. Nature. 497: 137-41. PMID 23604254 DOI: 10.1038/Nature12120 |
0.389 |
|
| 2013 |
Koide S, Huang J. Generation of high-performance binding proteins for peptide motifs by affinity clamping. Methods in Enzymology. 523: 285-302. PMID 23422435 DOI: 10.1016/B978-0-12-394292-0.00013-8 |
0.47 |
|
| 2013 |
Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nie R, Koide S. Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. Proceedings of the National Academy of Sciences of the United States of America. 110: 2099-104. PMID 23341609 DOI: 10.1073/Pnas.1219901110 |
0.358 |
|
| 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 |
0.421 |
|
| 2013 |
Persson H, Ye W, Wernimont A, Adams JJ, Koide A, Koide S, Lam R, Sidhu SS. CDR-H3 diversity is not required for antigen recognition by synthetic antibodies. Journal of Molecular Biology. 425: 803-11. PMID 23219464 DOI: 10.1016/J.Jmb.2012.11.037 |
0.318 |
|
| 2012 |
Nishikori S, Hattori T, Fuchs SM, Yasui N, Wojcik J, Koide A, Strahl BD, Koide S. Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. Journal of Molecular Biology. 424: 391-9. PMID 23041298 DOI: 10.1016/J.Jmb.2012.09.022 |
0.705 |
|
| 2012 |
Miller KR, Koide A, Leung B, Fitzsimmons J, Yoder B, Yuan H, Jay M, Sidhu SS, Koide S, Collins EJ. T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment. Plos One. 7: e43746. PMID 22916301 DOI: 10.1371/Journal.Pone.0043746 |
0.313 |
|
| 2012 |
Koide A, Koide S. Affinity maturation of single-domain antibodies by yeast surface display. Methods in Molecular Biology (Clifton, N.J.). 911: 431-43. PMID 22886267 DOI: 10.1007/978-1-61779-968-6_26 |
0.396 |
|
| 2012 |
Gilbreth RN, Koide S. Structural insights for engineering binding proteins based on non-antibody scaffolds. Current Opinion in Structural Biology. 22: 413-20. PMID 22749196 DOI: 10.1016/J.Sbi.2012.06.001 |
0.792 |
|
| 2012 |
Zhang X, Hoey RJ, Lin G, Koide A, Leung B, Ahn K, Dolios G, Paduch M, Ikeuchi T, Wang R, Li YM, Koide S, Sisodia SS. Identification of a tetratricopeptide repeat-like domain in the nicastrin subunit of γ-secretase using synthetic antibodies. Proceedings of the National Academy of Sciences of the United States of America. 109: 8534-9. PMID 22586122 DOI: 10.1073/Pnas.1202691109 |
0.448 |
|
| 2012 |
Kitahara R, Simorellis AK, Hata K, Maeno A, Yokoyama S, Koide S, Akasaka K. A delicate interplay of structure, dynamics, and thermodynamics for function: a high pressure NMR study of outer surface protein A. Biophysical Journal. 102: 916-26. PMID 22385863 DOI: 10.1016/J.Bpj.2011.12.010 |
0.373 |
|
| 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 |
0.518 |
|
| 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 |
0.785 |
|
| 2011 |
Grebien F, Hantschel O, Wojcik J, Kaupe I, Kovacic B, Wyrzucki AM, Gish GD, Cerny-Reiterer S, Koide A, Beug H, Pawson T, Valent P, Koide S, Superti-Furga G. Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis. Cell. 147: 306-19. PMID 22000011 DOI: 10.1016/J.Cell.2011.08.046 |
0.714 |
|
| 2011 |
Uysal S, Cuello LG, Cortes DM, Koide S, Kossiakoff AA, Perozo E. Mechanism of activation gating in the full-length KcsA K+ channel. Proceedings of the National Academy of Sciences of the United States of America. 108: 11896-9. PMID 21730186 DOI: 10.1073/Pnas.1105112108 |
0.3 |
|
| 2011 |
Gilbreth RN, Truong K, Madu I, Koide A, Wojcik JB, Li NS, Piccirilli JA, Chen Y, Koide S. Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design. Proceedings of the National Academy of Sciences of the United States of America. 108: 7751-6. PMID 21518904 DOI: 10.1073/Pnas.1102294108 |
0.786 |
|
| 2011 |
Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nature Structural & Molecular Biology. 18: 100-6. PMID 21151117 DOI: 10.1038/Nsmb.1945 |
0.323 |
|
| 2010 |
Shemon AN, Heil GL, Granovsky AE, Clark MM, McElheny D, Chimon A, Rosner MR, Koide S. Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands. Plos One. 5: e10479. PMID 20463977 DOI: 10.1371/Journal.Pone.0010479 |
0.464 |
|
| 2010 |
Wojcik J, Hantschel O, Grebien F, Kaupe I, Bennett KL, Barkinge J, Jones RB, Koide A, Superti-Furga G, Koide S. A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nature Structural & Molecular Biology. 17: 519-27. PMID 20357770 DOI: 10.1038/Nsmb.1793 |
0.75 |
|
| 2010 |
Huang J, Koide S. Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery. Acs Chemical Biology. 5: 273-7. PMID 20143785 DOI: 10.1021/Cb900284C |
0.386 |
|
| 2010 |
Biancalana M, Makabe K, Koide S. Minimalist design of water-soluble cross-beta architecture. Proceedings of the National Academy of Sciences of the United States of America. 107: 3469-74. PMID 20133689 DOI: 10.1073/Pnas.0912654107 |
0.333 |
|
| 2009 |
Takacs Z, Toups M, Kollewe A, Johnson E, Cuello LG, Driessens G, Biancalana M, Koide A, Ponte CG, Perozo E, Gajewski TF, Suarez-Kurtz G, Koide S, Goldstein SA. A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library. Proceedings of the National Academy of Sciences of the United States of America. 106: 22211-6. PMID 20007782 DOI: 10.1073/Pnas.0910123106 |
0.355 |
|
| 2009 |
Huang J, Nagy SS, Koide A, Rock RS, Koide S. A peptide tag system for facile purification and single-molecule immobilization. Biochemistry. 48: 11834-6. PMID 19928925 DOI: 10.1021/Bi901756N |
0.366 |
|
| 2009 |
Wu C, Biancalana M, Koide S, Shea JE. Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics. Journal of Molecular Biology. 394: 627-33. PMID 19799914 DOI: 10.1016/J.Jmb.2009.09.056 |
0.364 |
|
| 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 |
0.774 |
|
| 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 |
0.423 |
|
| 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 |
0.467 |
|
| 2009 |
Shemon AN, Eves EM, Clark MC, Heil G, Granovsky A, Zeng L, Imamoto A, Koide S, Rosner MR. Raf Kinase Inhibitory Protein protects cells against locostatin-mediated inhibition of migration. Plos One. 4: e6028. PMID 19551145 DOI: 10.1371/Journal.Pone.0006028 |
0.397 |
|
| 2009 |
Koide S. Engineering of recombinant crystallization chaperones. Current Opinion in Structural Biology. 19: 449-57. PMID 19477632 DOI: 10.1016/J.Sbi.2009.04.008 |
0.343 |
|
| 2009 |
Uysal S, Vásquez V, Tereshko V, Esaki K, Fellouse FA, Sidhu SS, Koide S, Perozo E, Kossiakoff A. Crystal structure of full-length KcsA in its closed conformation. Proceedings of the National Academy of Sciences of the United States of America. 106: 6644-9. PMID 19346472 DOI: 10.1073/Pnas.0810663106 |
0.362 |
|
| 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 |
0.496 |
|
| 2009 |
Granovsky AE, Clark MC, McElheny D, Heil G, Hong J, Liu X, Kim Y, Joachimiak G, Joachimiak A, Koide S, Rosner MR. Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism. Molecular and Cellular Biology. 29: 1306-20. PMID 19103740 DOI: 10.1128/Mcb.01271-08 |
0.425 |
|
| 2009 |
Biancalana M, Makabe K, Koide A, Koide S. Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies. Journal of Molecular Biology. 385: 1052-63. PMID 19038267 DOI: 10.1016/J.Jmb.2008.11.006 |
0.382 |
|
| 2009 |
Hantschel OD, Grebien F, Kaupe I, Kovacic B, Wojcik J, Gish GD, Koide S, Beug H, Pawson T, Superti-Furga G. The Bcr-Abl SH2-Kinase Domain Interface Is Critical for Leukemogenesis and An Additional Therapeutic Target in CML. Blood. 114: 37-37. DOI: 10.1182/Blood.V114.22.37.37 |
0.726 |
|
| 2009 |
Uysal S, Cuello LG, Jogini V, Cortes DM, Koide S, Perozo E, Kossiakoff A. Crystal Structure Of Full-length Kcsa Trapped In Open Conformation Reveals That C-terminal Domain Fine Tunes Activation And Coupled Inactivation Biophysical Journal. 96: 370a. DOI: 10.1016/J.Bpj.2008.12.1994 |
0.372 |
|
| 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 |
0.377 |
|
| 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 |
0.488 |
|
| 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 |
0.784 |
|
| 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 |
0.462 |
|
| 2008 |
Tereshko V, Uysal S, Koide A, Margalef K, Koide S, Kossiakoff AA. Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein Science : a Publication of the Protein Society. 17: 1175-87. PMID 18445622 DOI: 10.1110/Ps.034892.108 |
0.315 |
|
| 2008 |
Ye JD, Tereshko V, Frederiksen JK, Koide A, Fellouse FA, Sidhu SS, Koide S, Kossiakoff AA, Piccirilli JA. Synthetic antibodies for specific recognition and crystallization of structured RNA. Proceedings of the National Academy of Sciences of the United States of America. 105: 82-7. PMID 18162543 DOI: 10.1073/Pnas.0709082105 |
0.361 |
|
| 2008 |
Mallik B, Zhang L, Koide S, Morikis D. pH dependence of stability of the 10th human fibronectin type III domain: a computational study. Biotechnology Progress. 24: 48-55. PMID 17935345 DOI: 10.1021/Bp0700915 |
0.312 |
|
| 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 |
0.503 |
|
| 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 |
0.468 |
|
| 2007 |
Fellouse FA, Esaki K, Birtalan S, Raptis D, Cancasci VJ, Koide A, Jhurani P, Vasser M, Wiesmann C, Kossiakoff AA, Koide S, Sidhu SS. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. Journal of Molecular Biology. 373: 924-40. PMID 17825836 DOI: 10.1016/J.Jmb.2007.08.005 |
0.409 |
|
| 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 |
0.807 |
|
| 2007 |
Koide A, Zhao C, Naganuma M, Abrams J, Deighton-Collins S, Skafar DF, Koide S. Identification of regions within the F domain of the human estrogen receptor alpha that are important for modulating transactivation and protein-protein interactions. Molecular Endocrinology (Baltimore, Md.). 21: 829-42. PMID 17185393 DOI: 10.1210/Me.2006-0203 |
0.386 |
|
| 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 |
0.459 |
|
| 2006 |
Makabe K, Tereshko V, Gawlak G, Yan S, Koide S. Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering. Protein Science : a Publication of the Protein Society. 15: 1907-14. PMID 16823038 DOI: 10.1110/Ps.062246706 |
0.388 |
|
| 2006 |
Clark MC, McElheny D, Wojcik J, Kurutz J, Rosner MR, Koide S. NMR assignment of rat Raf kinase inhibitor protein. Journal of Biomolecular Nmr. 36: 4. PMID 16456706 DOI: 10.1007/S10858-005-4424-Y |
0.703 |
|
| 2006 |
Skafar DF, Koide S. Understanding the human estrogen receptor-alpha using targeted mutagenesis. Molecular and Cellular Endocrinology. 246: 83-90. PMID 16442702 DOI: 10.1016/J.Mce.2005.12.015 |
0.381 |
|
| 2006 |
Huang J, Koide A, Nettle KW, Greene GL, Koide S. Conformation-specific affinity purification of proteins using engineered binding proteins: Application to the estrogen receptor Protein Expression and Purification. 47: 348-354. PMID 16325424 DOI: 10.1016/J.Pep.2005.10.021 |
0.48 |
|
| 2006 |
McElheny D, Clark M, Wojcik J, Kurutz J, Rosner M, Koide S. Backbone/Sidechain assignments for RKIP. Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr6783 |
0.661 |
|
| 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 |
0.397 |
|
| 2005 |
Jha AK, Colubri A, Zaman MH, Koide S, Sosnick TR, Freed KF. Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry. 44: 9691-702. PMID 16008354 DOI: 10.1021/Bi0474822 |
0.325 |
|
| 2005 |
Koide S, Yang X, Huang X, Dunn JJ, Luft BJ. Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA. Journal of Molecular Biology. 350: 290-9. PMID 15935380 DOI: 10.1016/J.Jmb.2005.04.066 |
0.323 |
|
| 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 |
0.431 |
|
| 2004 |
Karatan E, Merguerian M, Han Z, Scholle MD, Koide S, Kay BK. Molecular recognition properties of FN3 monobodies that bind the Src SH3 domain. Chemistry & Biology. 11: 835-44. PMID 15217616 DOI: 10.1016/J.Chembiol.2004.04.009 |
0.426 |
|
| 2003 |
Hertadi R, Gruswitz F, Silver L, Koide A, Koide S, Arakawa H, Ikai A. Unfolding mechanics of multiple OspA substructures investigated with single molecule force spectroscopy. Journal of Molecular Biology. 333: 993-1002. PMID 14583195 DOI: 10.1016/J.Jmb.2003.09.010 |
0.326 |
|
| 2003 |
Zhao C, Koide A, Abrams J, Deighton-Collins S, Martinez A, Schwartz JA, Koide S, Skafar DF. Mutation of Leu-536 in human estrogen receptor-alpha alters the coupling between ligand binding, transcription activation, and receptor conformation. The Journal of Biological Chemistry. 278: 27278-86. PMID 12736255 DOI: 10.1074/Jbc.M303840200 |
0.362 |
|
| 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 |
0.485 |
|
| 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 |
0.419 |
|
| 2002 |
Pawley NH, Koide S, Nicholson LK. Backbone dynamics and thermodynamics of Borrelia outer surface protein A. Journal of Molecular Biology. 324: 991-1002. PMID 12470954 DOI: 10.1016/S0022-2836(02)01146-4 |
0.386 |
|
| 2002 |
Nakagawa T, Shimizu H, Link K, Koide A, Koide S, Tamura A. Calorimetric dissection of thermal unfolding of OspA, a predominantly beta-sheet protein containing a single-layer beta-sheet. Journal of Molecular Biology. 323: 751-62. PMID 12419262 DOI: 10.1016/S0022-2836(02)00974-9 |
0.33 |
|
| 2002 |
Koide A, Abbatiello S, Rothgery L, Koide S. Probing protein conformational changes in living cells by using designer binding proteins: Application to the estrogen receptor Proceedings of the National Academy of Sciences of the United States of America. 99: 1253-1258. PMID 11818562 DOI: 10.1073/Pnas.032665299 |
0.378 |
|
| 2001 |
Koide A, Jordan MR, Horner SR, Batori V, Koide S. Stabilization of a fibronectin type III domain by the removal of unfavorable electrostatic interactions on the protein surface. Biochemistry. 40: 10326-33. PMID 11513611 DOI: 10.1021/Bi010916Y |
0.377 |
|
| 2001 |
Pawley NH, Wang C, Koide S, Nicholson LK. An improved method for distinguishing between anisotropic tumbling and chemical exchange in analysis of 15N relaxation parameters. Journal of Biomolecular Nmr. 20: 149-65. PMID 11495246 DOI: 10.1023/A:1011249816560 |
0.329 |
|
| 2001 |
Huang X, Nakagawa T, Tamura A, Link K, Koide A, Koide S. Formation of the single-layer β-sheet of Borrelia burgdorferi OspA in the absence of the C-terminal capping globular domain Journal of Molecular Biology. 308: 367-375. PMID 11327773 DOI: 10.1006/Jmbi.2001.4579 |
0.321 |
|
| 2001 |
Yudt MR, Koide S. Preventing estrogen receptor action with dimer-interface peptides Steroids. 66: 549-558. PMID 11322963 DOI: 10.1016/S0039-128X(00)00224-5 |
0.328 |
|
| 2001 |
Kumaran D, Eswaramoorthy S, Luft BJ, Koide S, Dunn JJ, Lawson CL, Swaminathan S. Crystal structure of outer surface protein C (OspC) from the Lyme disease spirochete, Borrelia burgdorferi. The Embo Journal. 20: 971-8. PMID 11230121 DOI: 10.1093/Emboj/20.5.971 |
0.355 |
|
| 2000 |
Ding W, Huang X, Yang X, Dunn JJ, Luft BJ, Koide S, Lawson CL. Structural identification of a key protective B-cell epitope in Lyme disease antigen OspA. Journal of Molecular Biology. 302: 1153-64. PMID 11183781 DOI: 10.1006/Jmbi.2000.4119 |
0.343 |
|
| 2000 |
Koide S, Huang X, Link K, Koide A, Bu Z, Engelman DM. Design of single-layer beta-sheets without a hydrophobic core. Nature. 403: 456-60. PMID 10667801 DOI: 10.1038/35000255 |
0.316 |
|
| 1999 |
Koide S, Bu Z, Risal D, Pham TN, Nakagawa T, Tamura A, Engelman DM. Multistep denaturation of Borrelia burgdorferi OspA, a protein containing a single-layer beta-sheet. Biochemistry. 38: 4757-67. PMID 10200164 DOI: 10.1021/Bi982443+ |
0.347 |
|
| 1999 |
Nakagawa T, Tamura A, Akasaka K, Koide S, Huang X, Link K, Koide A. Multistep denaturation of Outer surface protein A (OspA) Seibutsu Butsuri. 39. DOI: 10.2142/Biophys.39.S163_1 |
0.327 |
|
| 1998 |
Bu Z, Koide S, Engelman DM. A solution SAXS study of Borrelia burgdorferi OspA, a protein containing a single-layer beta-sheet. Protein Science : a Publication of the Protein Society. 7: 2681-3. PMID 9865964 DOI: 10.1002/Pro.5560071223 |
0.341 |
|
| 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 |
0.486 |
|
| 1998 |
Pham TN, Koide S. NMR studies of Borrelia burgdorferi OspA, a 28 kDa protein containing a single-layer β-sheet Journal of Biomolecular Nmr. 11: 407-414. PMID 9691284 DOI: 10.1023/A:1008246908142 |
0.347 |
|
| 1998 |
Huang X, Yang X, Luft BJ, Koide S. NMR identification of epitopes of Lyme disease antigen OspA to monoclonal antibodies. Journal of Molecular Biology. 281: 61-7. PMID 9680475 DOI: 10.1006/Jmbi.1998.1930 |
0.345 |
|
| 1998 |
Pham TN, Koide A, Koide S. A stable single-layer β-sheet without a hydrophobic core Nature Structural Biology. 5: 115-119. PMID 9461076 DOI: 10.1038/Nsb0298-115 |
0.302 |
|
| 1997 |
Koide S, Bailev CW, Koide A. Directed evolution of fibronectin type iii domain to novel ligand binding proteins Faseb Journal. 11. |
0.325 |
|
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