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Current Medicinal Chemistry

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ISSN (Print): 0929-8673
ISSN (Online): 1875-533X

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Review Article

Development and Application of Computational Methods in Phage Display Technology

Author(s): Bifang He, Anthony Mackitz Dzisoo, Ratmir Derda and Jian Huang*

Volume 26, Issue 42, 2019

Page: [7672 - 7693] Pages: 22

DOI: 10.2174/0929867325666180629123117

Price: $65

Abstract

Background: Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display.

Methods: We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses.

Results: We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data.

Conclusion: The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.

Keywords: Phage display, mimotope, target-unrelated peptide, next-generation sequencing, epitope prediction, computational method, database.

« Previous Next »
[1]
Smith, G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science, 1985, 228(4705), 1315-1317.
[http://dx.doi.org/10.1126/science.4001944] [PMID: 4001944]
[2]
Bose, D.; Nahar, S.; Rai, M.K.; Ray, A.; Chakraborty, K.; Maiti, S. Selective inhibition of miR-21 by phage display screened peptide. Nucleic Acids Res., 2015, 43(8), 4342-4352.
[http://dx.doi.org/10.1093/nar/gkv185] [PMID: 25824952]
[3]
Zhang, Y.; He, B.; Liu, K.; Ning, L.; Luo, D.; Xu, K.; Zhu, W.; Wu, Z.; Huang, J.; Xu, X. A novel peptide specifically binding to VEGF receptor suppresses angiogenesis in vitro and in vivo. Signal Transduct. Target. Ther., 2017, 2, 17010.
[http://dx.doi.org/10.1038/sigtrans.2017.10] [PMID: 29263914]
[4]
Li, T.; Tu, W.; Liu, Y.; Zhou, P.; Cai, K.; Li, Z.; Liu, X.; Ning, N.; Huang, J.; Wang, S.; Huang, J.; Wang, H. A potential therapeutic peptide-based neutralizer that potently inhibits Shiga toxin 2 in vitro and in vivo. Sci. Rep., 2016, 6, 21837.
[http://dx.doi.org/10.1038/srep21837] [PMID: 26903273]
[5]
Guo, J.; Catchmark, J.M.; Mohamed, M.N.; Benesi, A.J.; Tien, M.; Kao, T.H.; Watts, H.D.; Kubicki, J.D. Identification and characterization of a cellulose binding heptapeptide revealed by phage display. Biomacromolecules, 2013, 14(6), 1795-1805.
[http://dx.doi.org/10.1021/bm4001876] [PMID: 23577599]
[6]
Joshi, B.P.; Dai, Z.; Gao, Z.; Lee, J.H.; Ghimire, N.; Chen, J.; Prabhu, A.; Wamsteker, E.J.; Kwon, R.S.; Elta, G.H.; Stoffel, E.M.; Pant, A.; Kaltenbach, T.; Soetikno, R.M.; Appelman, H.D.; Kuick, R.; Turgeon, D.K.; Wang, T.D. Detection of sessile serrated adenomas in the proximal colon using wide-field fluorescence endoscopy. Gastroenterology, 2017, 152(5), 1002-1013. e1009
[http://dx.doi.org/10.1053/j.gastro.2016.12.009]
[7]
Chen, C.; Liu, K.; Xu, Y.; Zhang, P.; Suo, Y.; Lu, Y.; Zhang, W.; Su, L.; Gu, Q.; Wang, H.; Gu, J.; Li, Z.; Xu, X. Anti-angiogenesis through noninvasive to minimally invasive intraocular delivery of the peptide CC12 identified by in vivo-directed evolution. Biomaterials, 2017, 112, 218-233.
[http://dx.doi.org/10.1016/j.biomaterials.2016.09.022] [PMID: 27768975]
[8]
Pande, J.; Szewczyk, M.M.; Grover, A.K. Phage display: concept, innovations, applications and future. Biotechnol. Adv., 2010, 28(6), 849-858.
[http://dx.doi.org/10.1016/j.biotechadv.2010.07.004] [PMID: 20659548]
[9]
He, B.; Mao, C.; Ru, B.; Han, H.; Zhou, P.; Huang, J. Epitope mapping of metuximab on CD147 using phage display and molecular docking. Comput. Math. Methods Med., 2013, 2013983829
[http://dx.doi.org/10.1155/2013/983829] [PMID: 23861727]
[10]
Huang, J.; He, B.; Zhou, P. Mimotope-based prediction of B-cell epitopes in: Methods Mol Biol; De, R.K.; Tomar, N., Eds.; Humana Press: New York, 2014, Vol. 1184, pp. 237-243.
[11]
Tong, A.H.; Drees, B.; Nardelli, G.; Bader, G.D.; Brannetti, B.; Castagnoli, L.; Evangelista, M.; Ferracuti, S.; Nelson, B.; Paoluzi, S.; Quondam, M.; Zucconi, A.; Hogue, C.W.; Fields, S.; Boone, C.; Cesareni, G. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science, 2002, 295(5553), 321-324.
[http://dx.doi.org/10.1126/science.1064987] [PMID: 11743162]
[12]
Huang, J.; Ru, B.; Dai, P. Prediction of protein interaction sites using mimotope analysis In: Protein-protein interactions-- computational and Experimental Tools; Cai, W., Ed.; Intech, 2012; pp. 189-206.
[http://dx.doi.org/ 10.5772/36694]
[13]
Nelson, A.L.; Dhimolea, E.; Reichert, J.M. Development trends for human monoclonal antibody therapeutics. Nat. Rev. Drug Discov., 2010, 9(10), 767-774.
[http://dx.doi.org/10.1038/nrd3229] [PMID: 20811384]
[14]
Liu, R.; Li, X.; Xiao, W.; Lam, K.S. Tumor-targeting peptides from combinatorial libraries. Adv. Drug Deliv. Rev., 2017, 110-111, 13-37.
[http://dx.doi.org/10.1016/j.addr.2016.05.009] [PMID: 27210583]
[15]
Martins, I.M.; Reis, R.L.; Azevedo, H.S. Phage display technology in biomaterials engineering: progress and opportunities for applications in regenerative medicine. ACS Chem. Biol., 2016, 11(11), 2962-2980.
[http://dx.doi.org/10.1021/acschembio.5b00717] [PMID: 27661443]
[16]
Lee, Y.J.; Yi, H.; Kim, W.J.; Kang, K.; Yun, D.S.; Strano, M.S.; Ceder, G.; Belcher, A.M. Fabricating genetically engineered high-power lithium-ion batteries using multiple virus genes. Science, 2009, 324(5930), 1051-1055.
[http://dx.doi.org/10.1126/science.1171541] [PMID: 19342549]
[17]
Ng, S.; Lin, E.; Kitov, P.I.; Tjhung, K.F.; Gerlits, O.O.; Deng, L.; Kasper, B.; Sood, A.; Paschal, B.M.; Zhang, P.; Ling, C.C.; Klassen, J.S.; Noren, C.J.; Mahal, L.K.; Woods, R.J.; Coates, L.; Derda, R. Genetically encoded fragment-based discovery of glycopeptide ligands for carbohydrate-binding proteins. J. Am. Chem. Soc., 2015, 137(16), 5248-5251.
[http://dx.doi.org/10.1021/ja511237n] [PMID: 25860443]
[18]
Glanville, J.; Zhai, W.; Berka, J.; Telman, D.; Huerta, G.; Mehta, G.R.; Ni, I.; Mei, L.; Sundar, P.D.; Day, G.M.; Cox, D.; Rajpal, A.; Pons, J. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc. Natl. Acad. Sci. USA, 2009, 106(48), 20216-20221.
[http://dx.doi.org/10.1073/pnas.0909775106] [PMID: 19875695]
[19]
’t Hoen, P.A.; Jirka, S.M.; Ten Broeke, B.R.; Schultes, E.A.; Aguilera, B.; Pang, K.H.; Heemskerk, H.; Aartsma-Rus, A.; van Ommen, G.J.; den Dunnen, J.T. Phage display screening without repetitious selection rounds. Anal. Biochem., 2012, 421(2), 622-631.
[http://dx.doi.org/10.1016/j.ab.2011.11.005] [PMID: 22178910]
[20]
Rentero Rebollo, I.; Sabisz, M.; Baeriswyl, V.; Heinis, C. Identification of target-binding peptide motifs by high-throughput sequencing of phage-selected peptides. Nucleic Acids Res., 2014, 42(22) e169
[http://dx.doi.org/10.1093/nar/gku940] [PMID: 25348396]
[21]
Ryvkin, A.; Ashkenazy, H.; Smelyanski, L.; Kaplan, G.; Penn, O.; Weiss-Ottolenghi, Y.; Privman, E.; Ngam, P.B.; Woodward, J.E.; May, G.D.; Bell, C.; Pupko, T.; Gershoni, J.M. Deep Panning: steps towards probing the IgOme. PLoS One, 2012, 7(8) e41469
[http://dx.doi.org/10.1371/journal.pone.0041469] [PMID: 22870226]
[22]
Ngubane, N.A.; Gresh, L.; Ioerger, T.R.; Sacchettini, J.C.; Zhang, Y.J.; Rubin, E.J.; Pym, A.; Khati, M. High-throughput sequencing enhanced phage display identifies peptides that bind mycobacteria. PLoS One, 2013, 8(11) e77844
[http://dx.doi.org/10.1371/journal.pone.0077844] [PMID: 24265677]
[23]
Van Blarcom, T.; Rossi, A.; Foletti, D.; Sundar, P.; Pitts, S.; Bee, C.; Melton Witt, J.; Melton, Z.; Hasa-Moreno, A.; Shaughnessy, L.; Telman, D.; Zhao, L.; Cheung, W.L.; Berka, J.; Zhai, W.; Strop, P.; Chaparro-Riggers, J.; Shelton, D.L.; Pons, J.; Rajpal, A. Precise and efficient antibody epitope determination through library design, yeast display and next-generation sequencing. J. Mol. Biol., 2015, 427(6 Pt B), 1513-1534.
[http://dx.doi.org/10.1016/j.jmb.2014.09.020] [PMID: 25284753]
[24]
Ibsen, K.N.; Daugherty, P.S. Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing. J. Immunol. Methods, 2017, 451, 28-36.
[http://dx.doi.org/10.1016/j.jim.2017.08.004] [PMID: 28827189]
[25]
Jalali-Yazdi, F.; Lai, L.H.; Takahashi, T.T.; Roberts, R.W. High-throughput measurement of binding kinetics by mRNA display and next-generation sequencing. Angew. Chem. Int. Ed. Engl., 2016, 55(12), 4007-4010.
[http://dx.doi.org/10.1002/anie.201600077] [PMID: 26914638]
[26]
Fujimori, S.; Hirai, N.; Ohashi, H.; Masuoka, K.; Nishikimi, A.; Fukui, Y.; Washio, T.; Oshikubo, T.; Yamashita, T.; Miyamoto-Sato, E. Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. Sci. Rep., 2012, 2, 691.
[http://dx.doi.org/10.1038/srep00691] [PMID: 23056904]
[27]
Olson, C.A.; Nie, J.; Diep, J.; Al-Shyoukh, I.; Takahashi, T.T.; Al-Mawsawi, L.Q.; Bolin, J.M.; Elwell, A.L.; Swanson, S.; Stewart, R.; Thomson, J.A.; Soh, H.T.; Roberts, R.W.; Sun, R. Single-round, multiplexed antibody mimetic design through mRNA display. Angew. Chem. Int. Ed. Engl., 2012, 51(50), 12449-12453.
[http://dx.doi.org/10.1002/anie.201207005] [PMID: 23125174]
[28]
Ravn, U.; Gueneau, F.; Baerlocher, L.; Osteras, M.; Desmurs, M.; Malinge, P.; Magistrelli, G.; Farinelli, L.; Kosco-Vilbois, M.H.; Fischer, N. By-passing in vitro screening--next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res., 2010, 38(21) e193
[http://dx.doi.org/10.1093/nar/gkq789] [PMID: 20846958]
[29]
Yang, W.; Yoon, A.; Lee, S.; Kim, S.; Han, J.; Chung, J. Next-generation sequencing enables the discovery of more diverse positive clones from a phage-displayed antibody library. Exp. Mol. Med., 2017, 49(3) e308
[http://dx.doi.org/10.1038/emm.2017.22] [PMID: 28336957]
[30]
Ernst, A.; Gfeller, D.; Kan, Z.; Seshagiri, S.; Kim, P.M.; Bader, G.D.; Sidhu, S.S. Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol. Biosyst., 2010, 6(10), 1782-1790.
[http://dx.doi.org/10.1039/c0mb00061b] [PMID: 20714644]
[31]
Cho, M.; Xiao, Y.; Nie, J.; Stewart, R.; Csordas, A.T.; Oh, S.S.; Thomson, J.A.; Soh, H.T. Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl. Acad. Sci. USA, 2010, 107(35), 15373-15378.
[http://dx.doi.org/10.1073/pnas.1009331107] [PMID: 20705898]
[32]
Derda, R.; Tang, S.K.; Li, S.C.; Ng, S.; Matochko, W.; Jafari, M.R. Diversity of phage-displayed libraries of peptides during panning and amplification. Molecules, 2011, 16(2), 1776-1803.
[http://dx.doi.org/10.3390/molecules16021776] [PMID: 21339712]
[33]
Matochko, W.L.; Cory Li, S.; Tang, S.K.; Derda, R. Prospective identification of parasitic sequences in phage display screens. Nucleic Acids Res., 2014, 42(3), 1784-1798.
[http://dx.doi.org/10.1093/nar/gkt1104] [PMID: 24217917]
[34]
Menendez, A.; Scott, J.K. The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies. Anal. Biochem., 2005, 336(2), 145-157.
[http://dx.doi.org/10.1016/j.ab.2004.09.048] [PMID: 15620878]
[35]
Nguyen, K.T.; Adamkiewicz, M.A.; Hebert, L.E.; Zygiel, E.M.; Boyle, H.R.; Martone, C.M.; Meléndez-Ríos, C.B.; Noren, K.A.; Noren, C.J.; Hall, M.F. Identification and characterization of mutant clones with enhanced propagation rates from phage-displayed peptide libraries. Anal. Biochem., 2014, 462, 35-43.
[http://dx.doi.org/10.1016/j.ab.2014.06.007] [PMID: 24952360]
[36]
Vodnik, M.; Strukelj, B.; Lunder, M. HWGMWSY, an unanticipated polystyrene binding peptide from random phage display libraries. Anal. Biochem., 2012, 424(2), 83-86.
[http://dx.doi.org/10.1016/j.ab.2012.02.013] [PMID: 22370277]
[37]
Vodnik, M.; Zager, U.; Strukelj, B.; Lunder, M. Phage display: selecting straws instead of a needle from a haystack. Molecules, 2011, 16(1), 790-817.
[http://dx.doi.org/10.3390/molecules16010790] [PMID: 21248664]
[38]
Thomas, W.D.; Golomb, M.; Smith, G.P. Corruption of phage display libraries by target-unrelated clones: diagnosis and countermeasures. Anal. Biochem., 2010, 407(2), 237-240.
[http://dx.doi.org/10.1016/j.ab.2010.07.037] [PMID: 20692225]
[39]
Brammer, L.A.; Bolduc, B.; Kass, J.L.; Felice, K.M.; Noren, C.J.; Hall, M.F. A target-unrelated peptide in an M13 phage display library traced to an advantageous mutation in the gene II ribosome-binding site. Anal. Biochem., 2008, 373(1), 88-98.
[http://dx.doi.org/10.1016/j.ab.2007.10.015] [PMID: 17976366]
[40]
Bakhshinejad, B.; Zade, H.M.; Shekarabi, H.S.; Neman, S. Phage display biopanning and isolation of target-unrelated peptides: in search of nonspecific binders hidden in a combinatorial library. Amino Acids, 2016, 48(12), 2699-2716.
[http://dx.doi.org/10.1007/s00726-016-2329-6] [PMID: 27650972]
[41]
Zade, H.M.; Keshavarz, R.; Shekarabi, H.S.Z.; Bakhshinejad, B. Biased selection of propagation-related TUPs from phage display peptide libraries. Amino Acids, 2017, 49(8), 1293-1308.
[http://dx.doi.org/10.1007/s00726-017-2452-z] [PMID: 28664268]
[42]
Zygiel, E.M.; Noren, K.A.; Adamkiewicz, M.A.; Aprile, R.J.; Bowditch, H.K.; Carroll, C.L.; Cerezo, M.A.S.; Dagher, A.M.; Hebert, C.R.; Hebert, L.E.; Mahame, G.M.; Milne, S.C.; Silvestri, K.M.; Sutherland, S.E.; Sylvia, A.M.; Taveira, C.N.; VanValkenburgh, D.J.; Noren, C.J.; Hall, M.F. Various mutations compensate for a deleterious lacZα insert in the replication enhancer of M13 bacteriophage. PLoS One, 2017, 12(4)e0176421
[http://dx.doi.org/10.1371/journal.pone.0176421] [PMID: 28445507]
[43]
Mandava, S.; Makowski, L.; Devarapalli, S.; Uzubell, J.; Rodi, D.J. RELIC--a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites. Proteomics, 2004, 4(5), 1439-1460.
[http://dx.doi.org/10.1002/pmic.200300680] [PMID: 15188413]
[44]
Huang, J.; Ru, B.; Li, S.; Lin, H.; Guo, F.B. SAROTUP: scanner and reporter of target-unrelated peptides. J. Biomed. Biotechnol., 2010, 2010101932
[http://dx.doi.org/10.1155/2010/101932] [PMID: 20339521]
[45]
Valuev, V.P.; Afonnikov, D.A.; Ponomarenko, M.P.; Milanesi, L.; Kolchanov, N.A. ASPD (Artificially selected proteins/peptides database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res., 2002, 30(1), 200-202.
[http://dx.doi.org/10.1093/nar/30.1.200] [PMID: 11752292]
[46]
Batori, V.; Friis, E.P.; Nielsen, H.; Roggen, E.L. An in silico method using an epitope motif database for predicting the location of antigenic determinants on proteins in a structural context. J. Mol. Recognit., 2006, 19(1), 21-29.
[http://dx.doi.org/10.1002/jmr.752] [PMID: 16193533]
[47]
Shtatland, T.; Guettler, D.; Kossodo, M.; Pivovarov, M.; Weissleder, R. PepBank--a database of peptides based on sequence text mining and public peptide data sources. BMC Bioinformatics, 2007, 8, 280.
[http://dx.doi.org/10.1186/1471-2105-8-280] [PMID: 17678535]
[48]
Kapoor, P.; Singh, H.; Gautam, A.; Chaudhary, K.; Kumar, R.; Raghava, G.P. TumorHoPe: a database of tumor homing peptides. PLoS One, 2012, 7(4)e35187
[http://dx.doi.org/10.1371/journal.pone.0035187] [PMID: 22523575]
[49]
Kodama, Y.; Shumway, M.; Leinonen, R. International Nucleotide Sequence Database Collaboration. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res., 2012, 40(Database issue), D54-D56.
[http://dx.doi.org/10.1093/nar/gkr854] [PMID: 22009675]
[50]
He, B.; Chai, G.; Duan, Y.; Yan, Z.; Qiu, L.; Zhang, H.; Liu, Z.; He, Q.; Han, K.; Ru, B.; Guo, F.B.; Ding, H.; Lin, H.; Wang, X.; Rao, N.; Zhou, P.; Huang, J. BDB: biopanning data bank. Nucleic Acids Res., 2016, 44(D1), D1127-D1132.
[http://dx.doi.org/10.1093/nar/gkv1100] [PMID: 26503249]
[51]
Ru, B.; Huang, J.; Dai, P.; Li, S.; Xia, Z.; Ding, H.; Lin, H.; Guo, F.; Wang, X.; Mimo, D.B. MimoDB: a new repository for mimotope data derived from phage display technology. Molecules, 2010, 15(11), 8279-8288.
[http://dx.doi.org/10.3390/molecules15118279] [PMID: 21079566]
[52]
Huang, J.; Ru, B.; Zhu, P.; Nie, F.; Yang, J.; Wang, X.; Dai, P.; Lin, H.; Guo, F.B.; Rao, N. MimoDB 2.0: a mimotope database and beyond. Nucleic Acids Res., 2012, 40(Database issue), D271-D277.
[http://dx.doi.org/10.1093/nar/gkr922] [PMID: 22053087]
[53]
Ru, B.; ’t Hoen, P.A.; Nie, F.; Lin, H.; Guo, F.B.; Huang, J. PhD7Faster: predicting clones propagating faster from the Ph.D.-7 phage display peptide library. J. Bioinform. Comput. Biol., 2014, 12(1) 1450005
[http://dx.doi.org/10.1142/S021972001450005X] [PMID: 24467763]
[54]
He, B.; Kang, J.; Ru, B.; Ding, H.; Zhou, P.; Huang, J. SABinder: A web service for predicting streptavidin-binding peptides. BioMed Res. Int., 2016, 2016 9175143
[http://dx.doi.org/10.1155/2016/9175143] [PMID: 27610387]
[55]
Li, N.; Kang, J.; Jiang, L.; He, B.; Lin, H.; Huang, J. PSBinder: A web service for predicting polystyrene surface-binding peptides. BioMed Res. Int., 2017, 2017 5761517
[http://dx.doi.org/10.1155/2017/5761517] [PMID: 29445741]
[56]
Huang, J.; Honda, W. CED: a conformational epitope database. BMC Immunol., 2006, 7, 7.
[http://dx.doi.org/10.1186/1471-2172-7-7] [PMID: 16603068]
[57]
Fleri, W.; Paul, S.; Dhanda, S.K.; Mahajan, S.; Xu, X.; Peters, B.; Sette, A. The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Front. Immunol., 2017, 8, 278.
[http://dx.doi.org/10.3389/fimmu.2017.00278] [PMID: 28352270]
[58]
Tang, Q.; Nie, F.; Kang, J.; Ding, H.; Zhou, P.; Huang, J. NIEluter: Predicting peptides eluted from HLA class I molecules. J. Immunol. Methods, 2015, 422, 22-27.
[http://dx.doi.org/10.1016/j.jim.2015.03.021] [PMID: 25862605]
[59]
Sun, P.; Ju, H.; Liu, Z.; Ning, Q.; Zhang, J.; Zhao, X.; Huang, Y.; Ma, Z.; Li, Y. Bioinformatics resources and tools for conformational B-cell epitope prediction. Comput. Math. Methods Med., 2013, 2013 943636
[http://dx.doi.org/10.1155/2013/943636] [PMID: 23970944]
[60]
Huang, J.; Ru, B.; Dai, P. Bioinformatics resources and tools for phage display. Molecules, 2011, 16(1), 694-709.
[http://dx.doi.org/10.3390/molecules16010694] [PMID: 21245805]
[61]
Mumey, B.M.; Bailey, B.W.; Kirkpatrick, B.; Jesaitis, A.J.; Angel, T.; Dratz, E.A. A new method for mapping discontinuous antibody epitopes to reveal structural features of proteins. J. Comput. Biol., 2003, 10(3-4), 555-567.
[http://dx.doi.org/10.1089/10665270360688183] [PMID: 12935344]
[62]
Mumey, B.; Ohler, N.; Angel, T.; Jesaitis, A.; Dratz, E. Filtering epitope alignments to improve protein surface prediction in: Frontiers of High Performance Computing and Networking–ISPA 2006 Workshops; Min, G.; Martino, B.D.; Yang, L.T; Rünger, M.G., Ed.; Springer, 2006, pp. 648-657.
[http://dx.doi.org/10.1007/11942634_67]
[63]
Moreau, V.; Granier, C.; Villard, S.; Laune, D.; Molina, F. Discontinuous epitope prediction based on mimotope analysis. Bioinformatics, 2006, 22(9), 1088-1095.
[http://dx.doi.org/10.1093/bioinformatics/btl012] [PMID: 16434442]
[64]
Halperin, R.F.; Stafford, P.; Emery, J.S.; Navalkar, K.A.; Johnston, S.A. GuiTope: an application for mapping random-sequence peptides to protein sequences. BMC Bioinformatics, 2012, 13, 1.
[http://dx.doi.org/10.1186/1471-2105-13-1] [PMID: 22214541]
[65]
Greenbaum, J.A.; Andersen, P.H.; Blythe, M.; Bui, H.H.; Cachau, R.E.; Crowe, J.; Davies, M.; Kolaskar, A.S.; Lund, O.; Morrison, S.; Mumey, B.; Ofran, Y.; Pellequer, J.L.; Pinilla, C.; Ponomarenko, J.V.; Raghava, G.P.; van Regenmortel, M.H.; Roggen, E.L.; Sette, A.; Schlessinger, A.; Sollner, J.; Zand, M.; Peters, B. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J. Mol. Recognit., 2007, 20(2), 75-82.
[http://dx.doi.org/10.1002/jmr.815] [PMID: 17205610]
[66]
Huang, J.; Gutteridge, A.; Honda, W.; Kanehisa, M. MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics, 2006, 7, 451.
[http://dx.doi.org/10.1186/1471-2105-7-451] [PMID: 17038191]
[67]
Castrignanò, T.; De Meo, P.D.; Carrabino, D.; Orsini, M.; Floris, M.; Tramontano, A. The MEPS server for identifying protein conformational epitopes. BMC Bioinformatics, 2007, 8(Suppl. 1), S6.
[http://dx.doi.org/10.1186/1471-2105-8-S1-S6] [PMID: 17430573]
[68]
Halperin, I.; Wolfson, H.; Nussinov, R. SiteLight: binding-site prediction using phage display libraries. Protein Sci., 2003, 12(7), 1344-1359.
[http://dx.doi.org/10.1110/ps.0237103] [PMID: 12824481]
[69]
Negi, S.S.; Braun, W. Automated detection of conformational epitopes using phage display Peptide sequences. Bioinform. Biol. Insights, 2009, 3, 71-81.
[http://dx.doi.org/10.4137/BBI.S2745] [PMID: 20140073]
[70]
Mayrose, I.; Shlomi, T.; Rubinstein, N.D.; Gershoni, J.M.; Ruppin, E.; Sharan, R.; Pupko, T. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res., 2007, 35(1), 69-78.
[http://dx.doi.org/10.1093/nar/gkl975] [PMID: 17151070]
[71]
Huang, Y.X.; Bao, Y.L.; Guo, S.Y.; Wang, Y.; Zhou, C.G.; Li, Y.X. Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis. BMC Bioinformatics, 2008, 9, 538.
[http://dx.doi.org/10.1186/1471-2105-9-538] [PMID: 19087303]
[72]
Bublil, E.M.; Freund, N.T.; Mayrose, I.; Penn, O.; Roitburd-Berman, A.; Rubinstein, N.D.; Pupko, T.; Gershoni, J.M. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins, 2007, 68(1), 294-304.
[http://dx.doi.org/10.1002/prot.21387] [PMID: 17427229]
[73]
Denisova, G.F.; Denisov, D.A.; Yeung, J.; Loeb, M.B.; Diamond, M.S.; Bramson, J.L. A novel computer algorithm improves antibody epitope prediction using affinity-selected mimotopes: a case study using monoclonal antibodies against the West Nile virus E protein. Mol. Immunol., 2008, 46(1), 125-134.
[http://dx.doi.org/10.1016/j.molimm.2008.07.020] [PMID: 18760481]
[74]
Chen, W.H.; Sun, P.P.; Lu, Y.; Guo, W.W.; Huang, Y.X.; Ma, Z.Q. MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries. BMC Bioinformatics, 2011, 12, 199.
[http://dx.doi.org/10.1186/1471-2105-12-199] [PMID: 21609501]
[75]
Chen, W.; Guo, W.W.; Huang, Y.; Ma, Z. PepMapper: a collaborative web tool for mapping epitopes from affinity-selected peptides. PLoS One, 2012, 7(5)e37869
[http://dx.doi.org/10.1371/journal.pone.0037869] [PMID: 22701536]
[76]
Sun, P.; Ju, H.; Zhang, B.; Gu, Y.; Liu, B.; Huang, Y.; Zhang, H.; Li, Y. Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis. BioMed Res. Int., 2015, 2015257030
[http://dx.doi.org/10.1155/2015/257030] [PMID: 25705652]
[77]
Sun, P.; Qi, J.; Zhao, Y.; Huang, Y.; Yang, G.; Ma, Z.; Li, Y. A novel conformational B-cell epitope prediction method based on mimotope and patch analysis. J. Theor. Biol., 2016, 394, 102-108.
[http://dx.doi.org/10.1016/j.jtbi.2016.01.021] [PMID: 26804644]
[78]
Enshell-Seijffers, D.; Denisov, D.; Groisman, B.; Smelyanski, L.; Meyuhas, R.; Gross, G.; Denisova, G.; Gershoni, J.M. The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. J. Mol. Biol., 2003, 334(1), 87-101.
[http://dx.doi.org/10.1016/j.jmb.2003.09.002] [PMID: 14596802]
[79]
Huang, J.; Xia, M.; Lin, H.; Guo, F. In: Bioinformatics and Biomedical Engineering; ICBBE 2009. 3rd International Conference on; IEEE, 2009; pp. 1-3.
[80]
Denisov, D.A.; Denisova, G.F.; Lelic, A.; Loeb, M.B.; Bramson, J.L. Deciphering epitope specificities within polyserum using affinity selection of random peptides and a novel algorithm based on pattern recognition theory. Mol. Immunol., 2009, 46(3), 429-436.
[http://dx.doi.org/10.1016/j.molimm.2008.10.013] [PMID: 19038455]
[81]
Denisova, G.F.; Denisov, D.A.; Bramson, J.L. Applying bioinformatics for antibody epitope prediction using affinity-selected mimotopes - relevance for vaccine design. Immunome Res., 2010, 6(Suppl. 2), S6.
[http://dx.doi.org/10.1186/1745-7580-6-S2-S6] [PMID: 21067548]
[82]
Sun, P.; Chen, W.; Huang, Y.; Wang, H.; Ma, Z.; Lv, Y. Epitope prediction based on random peptide library screening: benchmark dataset and prediction tools evaluation. Molecules, 2011, 16(6), 4971-4993.
[http://dx.doi.org/10.3390/molecules16064971] [PMID: 21681149]
[83]
Mayrose, I.; Penn, O.; Erez, E.; Rubinstein, N.D.; Shlomi, T.; Freund, N.T.; Bublil, E.M.; Ruppin, E.; Sharan, R.; Gershoni, J.M.; Martz, E.; Pupko, T. Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics, 2007, 23(23), 3244-3246.
[http://dx.doi.org/10.1093/bioinformatics/btm493] [PMID: 17977889]
[84]
Fowler, D.M.; Araya, C.L.; Fleishman, S.J.; Kellogg, E.H.; Stephany, J.J.; Baker, D.; Fields, S. High-resolution mapping of protein sequence-function relationships. Nat. Methods, 2010, 7(9), 741-746.
[http://dx.doi.org/10.1038/nmeth.1492] [PMID: 20711194]
[85]
Matochko, W.L.; Chu, K.; Jin, B.; Lee, S.W.; Whitesides, G.M.; Derda, R. Deep sequencing analysis of phage libraries using Illumina platform. Methods, 2012, 58(1), 47-55.
[http://dx.doi.org/10.1016/j.ymeth.2012.07.006] [PMID: 22819855]
[86]
He, B.; Tjhung, K.F.; Bennett, N.J.; Chou, Y.; Rau, A.; Huang, J.; Derda, R. Compositional bias in naïve and chemically-modified phage-displayed libraries uncovered by paired-end deep sequencing. Sci. Rep., 2018, 8(1), 1214.
[http://dx.doi.org/10.1038/s41598-018-19439-2] [PMID: 29352178]
[87]
Kim, T.; Tyndel, M.S.; Huang, H.; Sidhu, S.S.; Bader, G.D.; Gfeller, D.; Kim, P.M. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucleic Acids Res., 2012, 40(6)e47
[http://dx.doi.org/10.1093/nar/gkr1294] [PMID: 22210894]
[88]
Alam, K.K.; Chang, J.L.; Burke, D.H. FASTAptamer: A bioinformatic toolkit for high-throughput sequence analysis of combinatorial selections. Mol. Ther. Nucleic Acids, 2015, 4e230
[http://dx.doi.org/10.1038/mtna.2015.4] [PMID: 25734917]
[89]
Krejci, A.; Hupp, T.R.; Lexa, M.; Vojtesek, B.; Muller, P. Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. Bioinformatics, 2016, 32(1), 9-16.
[http://dx.doi.org/10.1093/bioinformatics/btv522] [PMID: 26342231]
[90]
Ma, W.; Noble, W.S.; Bailey, T.L. Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat. Protoc., 2014, 9(6), 1428-1450.
[http://dx.doi.org/10.1038/nprot.2014.083] [PMID: 24853928]
[91]
Fowler, D.M.; Araya, C.L.; Gerard, W.; Fields, S. Enrich: software for analysis of protein function by enrichment and depletion of variants. Bioinformatics, 2011, 27(24), 3430-3431.
[http://dx.doi.org/10.1093/bioinformatics/btr577] [PMID: 22006916]
[92]
Brinton, L.T.; Bauknight, D.K.; Dasa, S.S.; Kelly, K.A. PHASTpep: Analysis Software for Discovery of Cell-Selective Peptides via Phage Display and Next-Generation Sequencing. PLoS One, 2016, 11(5)e0155244
[http://dx.doi.org/10.1371/journal.pone.0155244] [PMID: 27186887]
[93]
Finn, R.D.; Clements, J.; Eddy, S.R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res, 2011, 39(Web Server issue), W29-W37.
[http://dx.doi.org/10.1093/nar/gkr367]
[94]
Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T.J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J.; Thompson, J.D.; Higgins, D.G. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol., 2011, 7, 539.
[http://dx.doi.org/10.1038/msb.2011.75] [PMID: 21988835]
[95]
Bailey, T.L.; Williams, N.; Misleh, C.; Li, W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res, 2006, 34(Web Server issue), W369-W373.
[http://dx.doi.org/10.1093/nar/gkl198] [PMID: 16845028]
[96]
Bailey, T.L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics, 2011, 27(12), 1653-1659.
[http://dx.doi.org/10.1093/bioinformatics/btr261] [PMID: 21543442]
[97]
Rubin, A.F.; Gelman, H.; Lucas, N.; Bajjalieh, S.M.; Papenfuss, A.T.; Speed, T.P.; Fowler, D.M. A statistical framework for analyzing deep mutational scanning data. Genome Biol., 2017, 18(1), 150.
[http://dx.doi.org/10.1186/s13059-017-1272-5] [PMID: 28784151]

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