2376 VTAPFRV(3) VIAKTRL(2) VPFKPIR(2) GMTMATP(2) GVGVPQR(2) AETVESC(1) DAFTRGT(1) GPPPLPK(1) IPSLPMR(1) LPVPIGY(1) MHTQDLM(1) MLNATSK(1) QDWNFKK(1) SGEIHFK(1) STFLPHP(1) YPTRELS(1) 16 Phage display (subtractive panning, competitive panning) 3 PMID:22555070 IgE of animal nr. 54 Allergen Ara h 1, clone P41B Not determined. Not determined. Ph.D.-7 phage display library (X7) In negative selection, the library was incubated with mouse-α-rat IgE. For positive selection, IgE of animal nr. 54, rat immunized with intact Ara h 1, were used and phages were eluted by competitive immunoscreening, by adding 25 μg allergen (intact Ara h 1). Three rounds of positive selection were performed. 2377 FTDTSWM(1) HGWPVPK(1) ITLQRTF(1) LHGRYFP(1) LTSPLRL(1) QGSQYTQ(1) TGSSNLY(1) TLLTTSP(1) TMTTPQQ(1) TTAPGKP(1) TTHYLHA(1) WPELYPV(1) YSYPGLT(1) 13 Phage display (subtractive panning, competitive panning) 3 PMID:22555070 IgE of animal nr. 54 Allergen Ara h 1, clone P41B Not determined. Not determined. Ph.D.-7 phage display library (X7) In negative selection, the library was incubated with mouse-α-rat IgE. For positive selection, IgE of animal nr. 54, rat immunized with intact Ara h 1, were used and phages were eluted by competitive immunoscreening, by adding 25 μg allergen (digested Ara h 1). Three rounds of positive selection were performed. 2378 GHTHKAM(1) GTSQFQL(1) HPPLLAT(1) HSMPTLH(1) HSSNAQV(1) HVPTVLS(1) IQQLKPP(1) ITPAALS(1) LNLDRKP(1) LPNPRNL(1) LQKTFMV(1) LSAKITL(1) LSTATVR(1) LTNSEWD(1) LTQQPPR(1) LWATRHI(1) LYALVPS(1) NQLLGST(1) QKPVYTR(1) QSFGVQL(1) SFPATKT(1) SHDVTPQ(1) STPLIPT(1) TPALFPY(1) TSPPRYL(1) VIHVKSP(1) VSHTQAN(1) YPRTISA(1) YSNAPTH(1) YSPHPYP(1) 30 Phage display (subtractive panning, competitive panning) 3 PMID:24365751 IgE of the peanut allergic patient no. 2208 Allergen Ara h 1, clone P41B Not determined. Not determined. Ph.D.-7 phage display library (X7) In negative selection, the library was incubated with rabbit-α-human IgE. For positive selection, IgG4 of the peanut allergic patient no. 2208 were used and phages were eluted by competitive immunoscreening, by adding phages were eluted by competitive immunoscreening by adding allergen (intact and digested Ara h 1) per 1 mL of beads. Three rounds of positive selection were performed. 2379 DLLSPAR(1) ISYQWPS(1) KVWVLPI(1) KVWYITS(1) LPARTVT(1) QYPRLTT(1) SHQIGPS(1) SLQEPWH(1) SPSFTQT(1) TDPTFAH(1) TLAQLPK(1) TRPLLPS(1) TVSPMTR(1) YHVPSYE(1) 14 Phage display (subtractive panning, competitive panning) 3 PMID:24365751 IgE of the peanut allergic patient no. 2209 Allergen Ara h 1, clone P41B Not determined. Not determined. Ph.D.-7 phage display library (X7) In negative selection, the library was incubated with rabbit-α-human IgE. For positive selection, IgG4 of the peanut allergic patient no. 2209 were used and phages were eluted by competitive immunoscreening, by adding phages were eluted by competitive immunoscreening by adding allergen (intact and digested Ara h 1) per 1 mL of beads. Three rounds of positive selection were performed. 2380 KCCYVPL(6) ANWTPYL(1) ESLQRPL(1) FAVQEAS(1) FHPTRYP(1) GLRWIAP(1) HITVPTR(1) HTNFTAP(1) HWHTSSR(1) KFTLHTP(1) KLWVIPV(1) LPLRLIL(1) LPSPWPY(1) LSLELAL(1) LTPYSSV(1) MATSTLA(1) MNYVPAP(1) MQPHYWQ(1) NHTYYQP(1) QTPESRS(1) SATMGKA(1) SFTTWLP(1) SLQSWLT(1) SMGIPRF(1) SPTLINL(1) TAPLHDP(1) TPLRTWP(1) TSTATSH(1) VPAHHLS(1) VSTTHIP(1) WSMYSAP(1) 31 Phage display (subtractive panning, competitive panning) 3 PMID:24365751 IgE of the peanut allergic patient no. 2305 Allergen Ara h 1, clone P41B Not determined. Not determined. Ph.D.-7 phage display library (X7) In negative selection, the library was incubated with rabbit-α-human IgE. For positive selection, IgG4 of the peanut allergic patient no. 2305 were used and phages were eluted by competitive immunoscreening, by adding phages were eluted by competitive immunoscreening by adding allergen (intact and digested Ara h 1) per 1 mL of beads. Three rounds of positive selection were performed. 2381 SVHLYHSTKTLR(4/11) QSYMERMYDAWP(4/11) DYMSALFMAHQT(3/11) 3 Phage display (common panning) 5 PMID:24460939 Interferon-induced, double-stranded RNA-activated protein kinase Eukaryotic translation initiation factor 2 subunit 1 Not determined. Not determined. Ph.D.-12 phage display library (X12) More than 100 clones were tested for their association towards PKRcat by phage-ELISA, and 11 clones with high binding index were subjected to DNA sequencing. Three sequences of high occurrence were obtained. By competitive phage-ELISA, the detected amount of phage was reduced with increasing concentration of P1 (DYMSALFMAHQT), P2 (SVHLYHSTKTLR), and P3 (QSYMERMYDAWP). Among the three peptides, P1 exhibited the most efficient binding with PKRcat. Besides, P1 and P2 inhibited PKR activity towards eIF2α in a concentration-dependent manner in vitro. P1 and P2 inhibit the enzymatic activity of PKR, and P1 is more efficient than P2 in vivo assay. 2382 LVFGTLLGQLRA(5) VSPSYYSWWNFR(3) F(3) NVSFR(2) CFMRL(1) CL(1) FAQMVIATNLSEM(1) FICIFRSSSVCG(1) IFVVLHFVCVHA(1) LPV(1) LSDHATFWASKV(1) PPSYLVLTGDSS(1) SVQYV(1) 13 Phage display (common panning) 6 PMID:21559518 Cyclosporin A, CsA Peptidyl-prolyl cis-trans isomerase A, PPIase A Not determined. Not determined. X12 T7 phage display library Due to the structural complexity of CsA, photoaffinity coupling method was applied to immobilize CsA. The highly reactive carbene induced by UV irradiation reacted with CsA, resulting in the production of immobilized CsA on solid surface in a nonspecific manner. Twenty two single phage clones were randomly pick out from the sixth panning elution. In order to validate the binding specificity of the phage, we amplified the phage #13 (LVFGTLLGQLRA) and measure the ratio of eluted phage titer with CsA and mock resins. The ratio of the phage #13 was 3.75, whereas randomly picked up phage was 1.00. These results indicated that the phage #13 specifically associated with CsA-immobilized resins. 2383 CDPRAADPC(1) CFGAPVSLC(1) CFPHLSRYC(1) CIWSPFFDC(1) CLYHDTHYC(1) CNPFCGSRC(1) CNPFLADPC(1) CPQDPKQWC(1) CPRSSLPSC(1) CPRSTSHLC(1) CPSPSRFPC(1) CQSTSGSSC(1) CSPDSLFPC(1) CSPWPLSYC(1) CTFSPLSVC(1) CTSPPLHAC(1) CVHSPFWPC(1) CYPGMLWTC(1) 18 Phage display (subtractive panning) 3 PMID:24256622 Serum of dogs with VL Leishmania infantum Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) In negative selection, the library was incubated with IgGs that had been purified from healthy dogs. The supernatant containing the clones that were not adhered to the IgGs was recovered and transferred to a new tube, and this procedure using IgGs from healthy dogs was repeated three times. After this, the supernatant was recovered and transferred to a new tube containing microspheres coupled to IgGs from T. cruzi-infected dogs, and this procedure of negative selection was also repeated three times. For positive selection, phage clones that did not adhere to the IgGs from T. cruzi-infected dogs were incubated with IgGs purified from serum samples of dogs with asymptomatic VL. The bound phage clones were transferred to a new tube containing IgGs that had been purified from serum samples of dogs with symptomatic VL. The process was repeated three times with serum samples of dogs with asymptomatic and symptomatic VL. Approximately 96 clones were randomly selected from individual colonies, and their DNA sequences were PCR amplified and sequenced. Eighteen clones had their sequences clearly identified, and an alignment showed that no identical consensus motif could be detected between them. 2384 WNNWQPQ(4) 1 Phage display (competitive panning) 3 PMID:24096567 Anti-BDE47 monoclonal antibody 1H2 2,2′,4,4′-tetrabromodiphenyl ether, BDE47 Not determined. Not determined. Ph.D.-7 phage display library (X7) The phage library was incubated with Mab 1H2 (20 μg/mL). Bound phages were eluted by incubation with PBS containing 100 ng/mL BDE47. The panning procedures were then repeated twice, but the Mab concentrations of 10 and 5 μg/mL were used for the second and the third panning, respectively. 2385 CWNNWQPQC(1) 1 Phage display (competitive panning) 3 PMID:24096567 Anti-BDE47 monoclonal antibody 1H2 2,2′,4,4′-tetrabromodiphenyl ether, BDE47 Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was incubated with Mab 1H2 (20 μg/mL). Bound phages were eluted by incubation with PBS containing 100 ng/mL BDE47. The panning procedures were then repeated twice, but the Mab concentrations of 10 and 5 μg/mL were used for the second and the third panning, respectively. 2386 GVSRLEILRAQL(4) GVSRKEILRAQG(2) 2 Phage display (competitive panning) 3 PMID:24096567 Anti-BDE47 monoclonal antibody 1H2 2,2′,4,4′-tetrabromodiphenyl ether, BDE47 Not determined. Not determined. Ph.D.-12 phage display library (X12) The phage library was incubated with Mab 1H2 (20 μg/mL). Bound phages were eluted by incubation with PBS containing 100 ng/mL BDE47. The panning procedures were then repeated twice, but the Mab concentrations of 10 and 5 μg/mL were used for the second and the third panning, respectively. 2387 VKLNDLR(1) 1 Phage display (subtractive panning) 3 PMID:24096567 Mab 1H2-BDE47 immunocomplex Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The phage library was firstly incubated with Mab 1H2 (20 μg/mL). Unbound phages were then incubated with Mab 1H2-BDE47 immunocomplex. The panning procedures were then repeated twice. 2388 CTELVTQLC(2) CNELVTQLC(2) CDELVRHLC(2) CQELVKHLC(1) CQELVPQLC(1) CQELVRHLC(1) 6 Phage display (subtractive panning) 3 PMID:24096567 Mab 1H2-BDE47 immunocomplex Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was firstly incubated with Mab 1H2 (20 μg/mL). Unbound phages were then incubated with Mab 1H2-BDE47 immunocomplex. The panning procedures were then repeated twice. 2389 WSEYDIPTPQIP(4) 1 Phage display (subtractive panning) 3 PMID:24096567 Mab 1H2-BDE47 immunocomplex Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The phage library was firstly incubated with Mab 1H2 (20 μg/mL). Unbound phages were then incubated with Mab 1H2-BDE47 immunocomplex. The panning procedures were then repeated twice. 2390 CVHRDTIYEYC(11) CFGRDTIFEVC(4) CVGRDTVHEFC(2) R-D-T-x(2)-E 3 Phage display (subtractive panning) 3 PMID:20152791 BDE47-polyclonal antibody immunocomplex Not determined. Not determined. Not determined. CX(7-11)C phage display library Phage peptide libraries were first counter selected by incubation in the wells coated with BDE 47 PAb in the absence of BDE 47. Unbound phage peptides were then transferred to other wells that had been incubated with 10 μg/ml BDE 47. As the panning proceeded, the amount of antibody for the selection was gradually decreased to remove weak binders by increased competition. Conversely, the amount of antibody for counter selection remained constant to remove nonspecific binders. In the last panning step, BDE 47 was added to the phage library after counter selection at a concentration of 10 ng/ml to competitively remove weak binders. A total of 17 phage clones were selected for screening by phage ELISA in the presence (50 ng/ml) or absence of BDE 47. All tested phage clones reacted with the immunocomplex, showing negligible cross-reactivity with the unbound antibody. 2391 CGTFAHPQC 1 Phage display (common panning) 3 PMID:18533899 Streptavidin Biotin Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was incubated with streptavidin. Elution by sonication was introduced. After 25 washings with PBST and 4 with glycine-HCl (0.2 M, pH 2.2), another 100 μl of glycine-HCl were added to the microtiter plate well, and the covered plate was immersed in a sonicator water bath (50 kHz) for 10 min. Three rounds of selection were performed. A lot of phage clones were recovered. Phage-displayed peptide sequences were determined if the ELISA signal of individual clones exceeded the blank by at least fourfold. So phage clones displayed peptide CGTFAHPQC were obtained. 2392 CGTFAHPQC 1 Phage display (competitive panning) 3 PMID:18533899 Streptavidin Biotin Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was incubated with streptavidin. After 25 washings with PBST and 4 with glycine-HCl (0.2 M, pH 2.2), 100 μl of 0.1 mM biotin was used for eluting. A lot of phage clones were recovered. Phage-displayed peptide sequences were determined if the ELISA signal of individual clones exceeded the blank by at least fourfold. So phage clones displayed peptide CGTFAHPQC were obtained. 2393 VVFTSWQDYLFWV 1 Phage display (common panning) 4 PMID:24225950 Proprotein convertase subtilisin/kexin type 9, PCSK9 Low-density lipoprotein receptor 2W2M,2W2N,2W2O,2W2P,2W2Q,3BPS,3GCW,3GCX,3M0C,3P5B,3P5C, Not determined. Linear-lib and Cyclic-lib M13 phage display library pool Phage pools of Linear-lib and Cyclic-lib library were cycled through rounds of binding selections. For round one, 130 nM of biotinylated PCSK9 was incubated with the phage library pool, and the phage-PCSK9 complex was captured by 200μl of Dynabeads® MyOne Streptavidin. For round two, the protocol was the same as round one except for using 65 nM of biotinylated PCSK9 and 100μl of Dynabeads. For round three, 26 nM of biotinylated PCSK9 was incubated with the amplified phage from the previous round, and the phage-PCSK9 complex was captured by NeutrAvidin-coated plates. Round four was identical with round three except for using Streptavidin-coated plates to capture biotin–PCSK9–phage complex. After four rounds of binding selection, several clones gave modest binding signals. Individual phage clones were analyzed in a high throughput spot phage ELISA using plate-immobilized PCSK9 as the target. Nonspecific binding was defined as phage particle binding to NeutrAvidin. Clones with phage binding signal to PCSK9 over 0.5 and signal/noise ratio of 5 were considered to be positive clones and were subjected to DNA sequence analysis. The peptides derived from these clones were synthesized and tested in the HepG2 LDL receptor degradation assay. Pep2 (VVFTSWQDYLFWV)derived from clone 2 was able to inhibit PCSK9-mediated LDL receptor degradation with low potency. 2394 QSHYRHISPAQV(20) TLAYARAYMVAP(2) QSHYRHISPDQV(1) QSHYRHISPARV(1) KSHYRHISPAKV(1) HHGHSPNVSQVR(1) GSFSTQVGSLHR(1) HTGTQSYVPRLR(1) ATPQNDLKTFPH(1) TQPETDLLRVQF(1) CITWPPTGLTYP(1) TFLETGPIYADG(1) LVPPTHRHWPVT(1) APPGNWRNYLMP(1) DNYSNYVPGTKP(1) SVSVGMKPSPRP(1) SLPNPFSVSSHG(1) YVHNPYHLPNPP(1) CRRLHTYLGPVT(1) 19 Phage display (competitive panning) 4 PMID:12898626 Soluble 37/48kDa oligomer formation of Aβ(1-42) Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) A commercially available phage-displayed peptide library (PhD12, New England Biolabs) was screened for peptide variants with affinity for synthetic bio-D-Aβ (1-42) immobilized on the surface of streptavidin-coated tubes. The phage-peptide suspension was transferred into a streptavidin-coated tube. To displace any streptavidin-binding phages, biotin (0.1 mM) was added. Eventually phages were eluted by 10-min incubation with glycine-HCl (0.8 mL, 0.2M, pH 2.2) and neutralized with Tris-HCl (0.2 mL, 1M, pH 9.1). After four rounds of selection and amplification, 39 randomly picked phages were subjected to DNA sequence analysis of the 5'-end of the gene coding for the minor coat protein. Upon translation into amino acid sequences, 23 of the resulting peptides showed strong sequence similarity. 2395 SEVGCRAGPLQLCEKYF 1 Phage display (common panning) 4 PMID:11075354 Insulin-like growth factor-binding protein 1, IGFBP-1 Insulin-like growth factor I, IGF-I 2DSQ, Not determined. SGTACX2GPX4CSLAGSP phage display library For the first three rounds of selection, IGFbp-1 was covalently linked to biotin using EZ-Link NHS-SS-biotin (Pierce). The biotin-SS-IGFbp-1 was first allowed to bind to immunosorbent plates coated with NeutrAvidin (Pierce). The fourth round of binding selection was carried out on immunosorbent plates directly coated with IGFbp-1. 2396 KDPVCGEGPLMRICERLF 1 Phage display (common panning) 4 PMID:11075354 Insulin-like growth factor-binding protein 1, IGFBP-1 Insulin-like growth factor I, IGF-I 2DSQ, Not determined. X4CX2GPX4CX4 phage display library For the first three rounds of selection, IGFbp-1 was covalently linked to biotin using EZ-Link NHS-SS-biotin (Pierce). The biotin-SS-IGFbp-1 was first allowed to bind to immunosorbent plates coated with NeutrAvidin (Pierce). The fourth round of binding selection was carried out on immunosorbent plates directly coated with IGFbp-1. 2397 EVDGRWWIVETFLAKWDHMA 1 Phage display (common panning) 4 PMID:11075354 Insulin-like growth factor-binding protein 1, IGFBP-1 Insulin-like growth factor I, IGF-I 2DSQ, Not determined. X20 M13 phage display library For the first three rounds of selection, IGFbp-1 was covalently linked to biotin using EZ-Link NHS-SS-biotin (Pierce). The biotin-SS-IGFbp-1 was first allowed to bind to immunosorbent plates coated with NeutrAvidin (Pierce). The fourth round of binding selection was carried out on immunosorbent plates directly coated with IGFbp-1. 2398 QGAMECEVVPRGVMCVLDSK 1 Phage display (common panning) 4 PMID:11075354 Insulin-like growth factor-binding protein 1, IGFBP-1 Insulin-like growth factor I, IGF-I 2DSQ, Not determined. X5CX8CX5 phage display library For the first three rounds of selection, IGFbp-1 was covalently linked to biotin using EZ-Link NHS-SS-biotin (Pierce). The biotin-SS-IGFbp-1 was first allowed to bind to immunosorbent plates coated with NeutrAvidin (Pierce). The fourth round of binding selection was carried out on immunosorbent plates directly coated with IGFbp-1. 2399 EVCVQIEWWCSH 1 Phage display (common panning) 4 PMID:11075354 Insulin-like growth factor-binding protein 1, IGFBP-1 Insulin-like growth factor I, IGF-I 2DSQ, Not determined. X2CX6CX2 phage display library For the first three rounds of selection, IGFbp-1 was covalently linked to biotin using EZ-Link NHS-SS-biotin (Pierce). The biotin-SS-IGFbp-1 was first allowed to bind to immunosorbent plates coated with NeutrAvidin (Pierce). The fourth round of binding selection was carried out on immunosorbent plates directly coated with IGFbp-1. 2400 YMDSGCAQGWEEYCMWECS 1 Phage display (common panning) 3 PMID:11075354 Bovine insulin-Like growth factor-binding protein 2, bIGFbp-2 Insulin-like growth factor I, IGF-I Not determined. Not determined. X5CX8CX5 phage display library BlGFbp-2 was coated directly onto immunosorbant plates. The library was subjected to three rounds of selection, using 100 mM HC1 elution, followed by neutralization. Phage from round 1 were amplified in E. coli before use in round 2. The eluted phage from round 2 were not amplified before use in round 3.