2626 VVACSWDWTMGAVVCYERI(1/39) 1 Phage display (subtractive panning) 3 PMID:15300809 Extracellular domain of receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Not determined. X4CX10CX4 fUSE5 phage display library In the first round, 0.9 μg ECDAP were incubated with anti-AP conjugated agarose beads on a nutator overnight at 4°C. The amplified phage library was incubated with anti-AP conjugated agarose beads alone for 2 hr on a nutator at room temperature to remove those phage specific for AP. The unbound phage were filtered with a 0.45 μm cellulose acetate syringe filter and incubated with ECDAP bound to beads on a nutator for 2 hr at room temperature. The unbound phage were removed by washing 5 times with PBS containing a cocktail of prokaryotic protease inhibitors (PPI) (Sigma). Additional two rounds of screening were performed. 2627 WTGWCLNPEESTWGFCTGSF(9/25) LNWECWYDYRLEAWDCRGDI(4/25) DTDMCWWWSREFGWECAGAG(2/25) VVACSWDWTMGAVVCYERI(1/25) 4 Phage display (subtractive panning) 3 PMID:15300809 Extracellular domain of receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Not determined. X4CX10CX4 fUSE5 phage display library In the first round, 0.9 μg ECDAP were incubated with anti-AP conjugated agarose beads on a nutator overnight at 4°C. The amplified phage library was incubated with anti-AP conjugated agarose beads alone for 2 hr on a nutator at room temperature to remove those phage specific for AP. The unbound phage were filtered with a 0.45 μm cellulose acetate syringe filter and incubated with ECDAP bound to beads on a nutator for 2 hr at room temperature. The unbound phage were removed by washing 5 times with PBS containing a cocktail of prokaryotic protease inhibitors (PPI) (Sigma). Additional two rounds of screening were performed. One clone (EC-1, displaying WTGWCLNPEESTWGFCTGSF) bound all preparations of ErbB2 including live cells and fresh frozen human breast cancer specimens. The synthetic peptide based on the deduced sequence of the EC-1 clone and its biotin-conjugated form retained binding affinity for purified ErbB2 and ErbB2 overexpressing cell lysates. EC-1 peptide was able to effectively inhibit the phosphorylation of ErbB2 on residues Y1248 and Y877 in a dose- and time-dependent manner. Furthermore, EC-1 peptide selectively inhibits the proliferation of ErbB2 overexpressing breast cancer cells. The linear portion of the cyclic EC-1 peptide was shown to be essential for binding ErbB2. In addition, 4 biased phage libraries were constructed allowing 4 different regions of the EC-1 peptide to have random sequence. 2628 VVACSWDWTMGAVVCYERI(1/25) WTGWCLNPEESTWGFCTGSF(1/25) 2 Phage display (subtractive panning) 1 PMID:15300809 Extracellular domain of receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Not determined. X4CX10CX4 fUSE5 phage display library In the first round, 20 μg CBECD was incubated in a polystyrene tube overnight at 4°C on a nutator. The isolated phage were pre-incubated in a casein blocked polystyrene tube to remove peptide-phage that bound to casein or polystyrene. The pre-cleared phage not bound to the casein/polystyrene tube were then added to the tube coated with CBECD and incubated on a nutator for 2 hr at room temperature. The non-bound phage were washed from beads by washing 5 times with PBS containing PPI. One clone (EC-1, displaying WTGWCLNPEESTWGFCTGSF) bound all preparations of ErbB2 including live cells and fresh frozen human breast cancer specimens. The synthetic peptide based on the deduced sequence of the EC-1 clone and its biotin-conjugated form retained binding affinity for purified ErbB2 and ErbB2 overexpressing cell lysates. EC-1 peptide was able to effectively inhibit the phosphorylation of ErbB2 on residues Y1248 and Y877 in a dose- and time-dependent manner. Furthermore, EC-1 peptide selectively inhibits the proliferation of ErbB2 overexpressing breast cancer cells. The linear portion of the cyclic EC-1 peptide was shown to be essential for binding ErbB2. In addition, 4 biased phage libraries were constructed allowing 4 different regions of the EC-1 peptide to have random sequence. 2629 WTGWCLNPEESTWGFCTGSF(8/25) LNWECWYDYRLEAWDCRGDI(4/25) DTDMCWWWSREFGWECAGAG(2/25) 3 Phage display (subtractive panning) 2 PMID:15300809 Extracellular domain of receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Not determined. X4CX10CX4 fUSE5 phage display library In the first round, 20 μg CBECD was incubated in a polystyrene tube overnight at 4°C on a nutator. The isolated phage were pre-incubated in a casein blocked polystyrene tube to remove peptide-phage that bound to casein or polystyrene. The pre-cleared phage not bound to the casein/polystyrene tube were then added to the tube coated with CBECD and incubated on a nutator for 2 hr at room temperature. The non-bound phage were washed from beads by washing 5 times with PBS containing PPI. Another one round of screening was performed. One clone (EC-1, displaying WTGWCLNPEESTWGFCTGSF) bound all preparations of ErbB2 including live cells and fresh frozen human breast cancer specimens. The synthetic peptide based on the deduced sequence of the EC-1 clone and its biotin-conjugated form retained binding affinity for purified ErbB2 and ErbB2 overexpressing cell lysates. EC-1 peptide was able to effectively inhibit the phosphorylation of ErbB2 on residues Y1248 and Y877 in a dose- and time-dependent manner. Furthermore, EC-1 peptide selectively inhibits the proliferation of ErbB2 overexpressing breast cancer cells. The linear portion of the cyclic EC-1 peptide was shown to be essential for binding ErbB2. In addition, 4 biased phage libraries were constructed allowing 4 different regions of the EC-1 peptide to have random sequence. 2630 VPQQSIP RGDVPP VRGRGSK NPGSSLG PGRGDL SRKDV QRSGRGP LPNRSQI VLGRGK DLISSK 10 Phage display (subtractive panning) 3 PMID:15569135 IA/IAA-enriched immunoglobulin G from REM-A Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) After this first round of‘positive' selection with IAA sera, 'negative' selection was achieved whereby phages not specifically reactive with IAA sera were removed using 100 μg of IgG prepared from pooled normal sera. The amplified eluate was enriched by two further rounds of positive selection, negative selection, and amplification. 2631 LDQRSSK PGSRLQP LQPISN VIQGSRL QVRGGS NIKSSLP PDGSRLV QQSPPI VQLNPD ARSKPN 10 Phage display (subtractive panning) 3 PMID:15569135 IA/IAA-enriched immunoglobulin G from REM-B Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) After this first round of‘positive' selection with IAA sera, 'negative' selection was achieved whereby phages not specifically reactive with IAA sera were removed using 100 μg of IgG prepared from pooled normal sera. The amplified eluate was enriched by two further rounds of positive selection, negative selection, and amplification. 2632 VPQQSIP RGDVPP VGERGSK NPGSSLG GERAKRS STGERIQ QGERSGP LPGERQI DLISSK VLGERK 10 Phage display (subtractive panning) 3 PMID:15569135 IA/IAA-enriched immunoglobulin G from NREM-A Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) After this first round of‘positive' selection with IAA sera, 'negative' selection was achieved whereby phages not specifically reactive with IAA sera were removed using 100 μg of IgG prepared from pooled normal sera. The amplified eluate was enriched by two further rounds of positive selection, negative selection, and amplification. 2633 LDQSRLK PGTRLQP PSRLVNQ VIQGSQL QVRGGS NIKSSLP LQPISN QQSRLI VSRSLLD ARSKPN 10 Phage display (subtractive panning) 3 PMID:15569135 IA/IAA-enriched immunoglobulin G from NREM-B Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) After this first round of‘positive' selection with IAA sera, 'negative' selection was achieved whereby phages not specifically reactive with IAA sera were removed using 100 μg of IgG prepared from pooled normal sera. The amplified eluate was enriched by two further rounds of positive selection, negative selection, and amplification. 2634 AKWSDLWLAAPG EQNSYWKQLFLE HHMKDFATLFST NTNAFSRLFYPS HKFQELYQSTTP DHSKLYSLLQSS [FW]-x(2)-L-[FW], F-x(2)-L-Y 6 Phage display (common panning) 3 PMID:12714604 RAR-DBD-LBD Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Each round of panning was performed on streptavidin-coated wells of a 96-well enzyme-linked immunosorbent assay plate. 2635 TATPGTWYNLWL EPNSYWKQLFLE TRQPPTTFYSLF QNFKSLFSATLP SSQRFVDLFSND HTPTTFSRLWTP DRDPSKFSLLWH QPKHFTELYFKS TSRFSHFQELYS STTKFGTLYWEN [FW]-x(2)-L-[FW] 10 Phage display (common panning) 4 PMID:12714604 RAR-DBD-LBD Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) 2636 TGGGVSLLLHLLNTEQGES RRDDFPLLISLLKDGALSQ YGLKMSLLESLLREDISTV MSYDMLSLYPLLTNSLLEV FPAEFPLLTYLLERQGMDE VESEFPYLLSLLGEVSPQP 6 Phage display (common panning) 3 PMID:11117531 Estrogen receptor beta, ER-beta Not determined. Not determined. Not determined. (X)7LXXLL(X)7 library Each round of panning was performed in the absence of 17β-estradiol. 2637 VSSEGRLLIDLLVDGQQSE DTPQSPLLWGLLSSDRVEG GGTQDGYLWSLLTGMPEVS SLPEEGFLMKLLTLEGDAE VMGNNPILVSLLEEPSEEP VLVEHPILGGLLSTRVDSS QTPLLEQLLTEHIQQG 7 Phage display (common panning) 3 PMID:11117531 Estrogen receptor beta, ER-beta Not determined. Not determined. Not determined. (X)7LXXLL(X)7 library Each round of panning was performed in the presence of 17β-estradiol. 2638 EDGGSLLRWYLEHEFGGGGSGK EDGGSPLWQIFSRELGGGGSK EDGGSWVEWVEEERRGGGGK EDGGSRRFTFQYGSV EDGGSLFERVWLREL 5 Phage display (common panning) 2-3 PMID:14976226 Estrogen receptor, ER Not determined. Not determined. Not determined. fGWX10 phage display library Biotinylated ERα LBD or biotinylated ERα FL was immobilized on a neutravidin-coated microtiter plate well. Each round od panning was performed on neutravidin-coated microtiter plate well. 2639 EYHEKRWLEGHIHHRIKSLLENS(16) QETIQRWLRGHIQRELGTMELKD(14) HSTTLTGLASIIRERILTELRDE(1) PENFRQALRAHIADLITNQDYRS(1) 4 Phage display (common panning) 3 PMID:12145334 Vitellogenin estrogen response element (ERE) Not determined. Not determined. Not determined. X7LXX[HI]IXXX[IL]X7 CoRNR box phage display library The target was biotinylated. Each round of panning was performed on streptavidin-coated Immulon 4 plates. 2640 ELFDAFQLRQLILRGLQDDIPYH(16) EYHEKRWLEGHIHHRIKSLLENS(1) 2 Phage display (common panning) 3 PMID:12145334 Estrogen receptor beta, ER-beta Not determined. Not determined. Not determined. X7LXX[HI]IXXX[IL]X7 CoRNR box phage display library The real target is ERβ treated with 4-hydroxytamoxifen. The target was biotinylated. Each round of panning was performed on streptavidin-coated Immulon 4 plates. 2641 EMEWMKALRQHISGELRRNYTEE(5) AAYDPAALNNNIRYALVKHSQIK(3) KWESLDALQGLISSHLSAMGPIP(2) FMNNGVLLATNIENLLRTQPGSN(1) NAAPRTALSHHIHSDLLDGPTTT(1) PKTPGVPLNPLISPEITSDTSML(1) NTYNTGALRFNIVESIWASKKLR(1) VPRFTKGLVGNIPLAIDTNSGTV(1) ESERANLLKEHIKMTLPEERKKT(1) NVIAQPTLASIIPPSLKRQSEAR(1) SPFTQVTLKGNIAPSIVGSQGMA(1) PIAHRVNLRHNITEDITLSHRFL(1) IDDGHPHLWKNIWDTLDKPGLGA(1) FKPGTSSLDTHIPLGLNKSFHHN(1) NQGNTKELLGNINYFLTHHTVPA(1) LTYPIRELKMNITSGIRLDKRVL(1) HKDSQLTLANNIMGQLSSTGGKH(1) WDVGEIRLRRHIKMPLSEEAIAE(1) SHYEKYSLPGIIVRKISTTDWRP(1) QHQNRQQLGSNIAATLPGKRESV(1) KSQTKAELPYLIGKQITKNQPEQ(1) DALDNQRLLGNIDNVLKVTNPNA(1) GQSARFALSQHIPSKIYDHPRPN(1) RAVHERALNPLILDRLLHELKSE(1) 24 Phage display (common panning) 3 PMID:12145334 Estrogen receptor beta, ER-beta Not determined. Not determined. Not determined. X7LXX[HI]IXXX[IL]X7 CoRNR box phage display library The real target is ERβ treated with ICI 182, 780. The target was biotinylated. Each round of panning was performed on streptavidin-coated Immulon 4 plates. 2642 DWEYSVWLSN(23) STEHSEADLW(8) LYFEDYRCEL(3) DWDYGALMWA(1) YSDWDYSEGL(1) [DE]-W-[DE]-Y-[SG] 5 Phage display (common panning) 3/4 PMID:9050886 Anti-dsDNA monoclonal antibody R4A Not determined. Not determined. Not determined. L100 phage display library (X10) For the first round of selection, 50 μl of streptavidin-coated magnetic beads were incubated with 100 μl of 5 μM biotinylated protein G for 1 hr at room temperature with agitation. In subsequent rounds of selection, 10 μl of streptavidin beads and 0.05 μM of biotinylated protein G were used. The streptavidin bead/biotinylated protein G complex was combined with the phage/antibody mixture and incubated. 2643 WCEADYGRCP(23) FSDCYHSGCP(3) VPVCDWELNC(1) 3 Phage display (common panning) 3/4 PMID:9050886 Anti-dsDNA monoclonal antibody R4A Not determined. Not determined. Not determined. L100 phage display library (X10) For the first round of selection, 50 μl of streptavidin-coated magnetic beads were incubated with 100 μl of 5 μM biotinylated protein G for 1 hr at room temperature with agitation. In subsequent rounds of selection, 10 μl of streptavidin beads and 0.05 μM of biotinylated protein G were used. The streptavidin bead/biotinylated protein G complex was combined with the phage/antibody mixture and incubated. 2644 SLDELDWDSM(4) RHEDGDWPRV(1) LLDDGFWPRV(1) CGVDGRWPRW(1) SLISDEWPRW(1) DGEWPREGWS(1) EDLEGEWPMR(1) [DE]-G-[DE]-W-P-R 7 Phage display (common panning) 3/4 PMID:9050886 Anti-dsDNA monoclonal antibody 52b3 Not determined. Not determined. Not determined. L100 phage display library (X10) For the first round of selection, 50 μl of streptavidin-coated magnetic beads were incubated with 100 μl of 5 μM biotinylated protein G for 1 hr at room temperature with agitation. In subsequent rounds of selection, 10 μl of streptavidin beads and 0.05 μM of biotinylated protein G were used. The streptavidin bead/biotinylated protein G complex was combined with the phage/antibody mixture and incubated. 2645 HIPAYATHV[1.40] EHFWEQRPR[1.11] WLVQSPPW[1.14] QSHFLLQGT[1.12] KRHFLSQRQ[1.23] HFLSQNFFG[1.66] WGPFQYAAG[1.98] LLRQARERP[0.96] PPLSQRRAL[1.46] TRQQNNPER[0.90] 10 Phage display (common panning) 2 PMID:9368618 Anti-the 0-Ag of the S. flexneri serotype 5a LPS monoclonal antibody C5 O-antigen of lipopolysaccharide, O-Ag of LPS Not determined. Not determined. pVIII-9aa phage display library (X9) ELISA Wild-type phage (pwt) (cross-reacting with the Shigeffa LPS core moiety) was used as the negative control and its absorbance value is 0.05. The absorbance is shown. In the first round, the mAb was incubated at 1 μM concentration overnight at 4°C with 1.0e10 Amp(R) tranducing unit (TU) of library in a total volume of 10 pl. The mixture was incubated with 0.25 μg of a biotin-conjugated goat antimouse IgA secondary antibody ((α-chain specific), which was previously pre-adsorbed overnight at 4°C with 2.0e11 phage particles of UV-killed M13K07 to prevent nonspecific binding, and then the phage-mAb-secondary Ab complexes were tethered on streptavidin-coated dishes. The second round of affinity selection was carried out in the same way, but using 10 nM or 0.1 nM concentrations of mAb and proportionally lower amounts of the secondary antibody. 2646 KVPAWARRL[0.18] KVPPWARTA[0.51] 2 Phage display (common panning) 2 PMID:9368618 Anti-the 0-Ag of the S. flexneri serotype 5a LPS monoclonal antibody I3 O-antigen of lipopolysaccharide, O-Ag of LPS Not determined. Not determined. pVIII-9aa phage display library (X9) ELISA Wild-type phage (pwt) (cross-reacting with the Shigeffa LPS core moiety) was used as the negative control and its absorbance value is 0.05. The absorbance is shown. In the first round, the mAb was incubated at 1 μM concentration overnight at 4°C with 1.0e10 Amp(R) tranducing unit (TU) of library in a total volume of 10 pl. The mixture was incubated with 0.25 μg of a biotin-conjugated goat antimouse IgA secondary antibody ((α-chain specific), which was previously pre-adsorbed overnight at 4°C with 2.0e11 phage particles of UV-killed M13K07 to prevent nonspecific binding, and then the phage-mAb-secondary Ab complexes were tethered on streptavidin-coated dishes. The second round of affinity selection was carried out in the same way, but using 10 nM or 0.1 nM concentrations of mAb and proportionally lower amounts of the secondary antibody. 2647 CGSPLRQRRSC[0.20] CGSPLRQRSLC[0.19] CSQGRWPWURC[0.31] CYKPLGALTHC[0.85] 4 Phage display (common panning) 2 PMID:9368618 Anti-the 0-Ag of the S. flexneri serotype 5a LPS monoclonal antibody I3 O-antigen of lipopolysaccharide, O-Ag of LPS Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) ELISA Wild-type phage (pwt) (cross-reacting with the Shigeffa LPS core moiety) was used as the negative control and its absorbance value is 0.05. The absorbance is shown. In the first round, the mAb was incubated at 1 μM concentration overnight at 4°C with 1.0e10 Amp(R) tranducing unit (TU) of library in a total volume of 10 pl. The mixture was incubated with 0.25 μg of a biotin-conjugated goat antimouse IgA secondary antibody ((α-chain specific), which was previously pre-adsorbed overnight at 4°C with 2.0e11 phage particles of UV-killed M13K07 to prevent nonspecific binding, and then the phage-mAb-secondary Ab complexes were tethered on streptavidin-coated dishes. The second round of affinity selection was carried out in the same way, but using 10 nM or 0.1 nM concentrations of mAb and proportionally lower amounts of the secondary antibody. 2648 CTRGHFLQNRC[1.79] CRRHFLEQRGC[1.92] CSPHFFNQIRC[1.26] 3 Phage display (common panning) 2 PMID:9368618 Anti-the 0-Ag of the S. flexneri serotype 5a LPS monoclonal antibody C5 O-antigen of lipopolysaccharide, O-Ag of LPS Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) ELISA Wild-type phage (pwt) (cross-reacting with the Shigeffa LPS core moiety) was used as the negative control and its absorbance value is 0.05. The absorbance is shown. In the first round, the mAb was incubated at 1 μM concentration overnight at 4°C with 1.0e10 Amp(R) tranducing unit (TU) of library in a total volume of 10 pl. The mixture was incubated with 0.25 μg of a biotin-conjugated goat antimouse IgA secondary antibody ((α-chain specific), which was previously pre-adsorbed overnight at 4°C with 2.0e11 phage particles of UV-killed M13K07 to prevent nonspecific binding, and then the phage-mAb-secondary Ab complexes were tethered on streptavidin-coated dishes. The second round of affinity selection was carried out in the same way, but using 10 nM or 0.1 nM concentrations of mAb and proportionally lower amounts of the secondary antibody. 2649 YRNQYQPPPYASSQ LQRDRPPPPYPTP SYYRQPPPPYPTSA SQRGTPPPPYPFAA SRQVLEPFYPQKA RCWWGPPPPYPKVA LMRIDPPPPYPSM WWNYDEPPAYWSTI PWVLEPPPPYPGT RAAGRLPPPYWELE WQRCTSPPAYYDAI EWKREPPPEYRPPP x-P-P-x-Y 12 Phage display (common panning) 3 PMID:9224934 Yorkie homolog Not determined. Not determined. Not determined. SSX6PPX6SR M13 phage display library 2650 DQLRDEPPAYWDVV QMEREPPPPYPQPS GWGEVPPPPYRPKE RDGYGPPPPYRPPT RAESGSPPPYPLES ASAKIMPPPYPSNN WLRRGIPPPYPSTE GLYQGPPPTYPTR SHERIPPPPYPHS RISRYPPPAYNTDN RGELSNPPPYPPLR SSRQAPPPPYPRDY x-P-P-x-Y 12 Phage display (common panning) 3 PMID:9224934 Yorkie homolog Not determined. Not determined. Not determined. SSX6PPX6SR M13 phage display library