1201 CPALLCRC(1) CIPALWSFC(2) CAARLWQWC(1) CTA(A/P)LWRIC(1) CTAALWRIC(2) CTATLWRIC(2) 6 Phage display (common panning) 6 PMID:9680646 Chymotrypsinogen A Not determined. Not determined. Not determined. CX7C phage display library Phage particles were incubated with biotinylated alpha-chymotrypsin in pH 6.5 buffer. Streptavidin-agarose (50 μl) was blocked with 20 μl 50 mg/ml dialyzed BSA in TBS for 60 min and added to each of the three selection vials. 1202 CSASLWFLC(13) CS(G/E)TLWS(K/T)C(1) 2 Phage display (common panning) 6 PMID:9680646 Chymotrypsinogen A Not determined. Not determined. Not determined. CX7C phage display library Phage particles were incubated with biotinylated alpha-chymotrypsin in pH 7.0 buffer. Streptavidin-agarose (50 μl) was blocked with 20 μl 50 mg/ml dialyzed BSA in TBS for 60 min and added to each of the three selection vials. 1203 CCFSWRCRC(5) CWGSWRCRC(1) CWSPKRCRC(1) 3 Phage display (common panning) 6 PMID:9680646 Chymotrypsinogen A Not determined. Not determined. Not determined. CX7C phage display library Phage particles were incubated with biotinylated alpha-chymotrypsin in pH 7.5 buffer. Streptavidin-agarose (50 μl) was blocked with 20 μl 50 mg/ml dialyzed BSA in TBS for 60 min and added to each of the three selection vials. The oxidized form of the synthetic peptide CCFSWRCRC, selected at pH 7.5, could completely inhibit the enzymatic activity of alpha-chymotrypsin. The structurally related enzymes trypsin (bovine) and elastase (porcine) were only marginally inhibited by the same peptide under the same conditions. 1204 RRLPFGSQM(4)[+++] RYAFGSQIA(2)[++] RRLPFGSSL(1)[+] RAGRFGYQR(1)[+] TRSFGIQAT(1)[+] SRLAFGDQL(1)[+] HEHTFGRQW(1)[+++] TRAFGNEAT(1)[+] RAAPFGNQW(1)[++] HRLAFGQNT(1)[+++] HRLAFGQYT(1)[+++] F-G-x-Q 11 Phage display (subtractive panning) 3 PMID:9693968 Anti-collagen alpha-1(II) chain monoclonal antibody CII-C1 Collagen alpha-1(II) chain Not determined. Not determined. pVIII-9aa phage display library (X9) ELISA Phagotopes selected by biopanning with the mAbs were tested by ELISA for reactivity with CII-C1. The negative control was wild type fl bacteriophage (wt fl). After the first round of positive selection, there was a negative selection step in which phage not specifically reactive with the monoclonal antibody used for selection were removed using magnetic beads coated with anti-mouse immunoglobulin. 1205 CIAPKRHNSAC[++] CESAQRPFGCC[++] 2 Phage display (subtractive panning) 3 PMID:9693968 Anti-collagen alpha-1(II) chain monoclonal antibody CII-C1 Collagen alpha-1(II) chain Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) ELISA Phagotopes selected by biopanning with the mAbs were tested by ELISA for reactivity with CII-C1. The negative control was wild type fl bacteriophage (wt fl). After the first round of positive selection, there was a negative selection step in which phage not specifically reactive with the monoclonal antibody used for selection were removed using magnetic beads coated with anti-mouse immunoglobulin. 1206 LSFAAEGEF(1)[NT] YKLTCSSAQ(1)[NT] ARLSSAVVK(1)[-] GHSLCSCIP(1)[-] GSRFNKVPS(1)[-] KKKTVLPDL(1)[-] LKIGDFPAG(1)[-] SRRTLMSGA(1)[-] TKIRNVAGM(1)[-] 9 Phage display (subtractive panning) 3 PMID:9693968 Anti-chicken GAD monoclonal antibody GAD1 Glutamate decarboxylase 67 Not determined. Not determined. pVIII-9aa phage display library (X9) Phagotopes selected by biopanning with the mAbs were tested by ELISA for reactivity with GAD1. The negative control was wild type fl bacteriophage (wt fl). NT represents not tested. After the first round of positive selection, there was a negative selection step in which phage not specifically reactive with the monoclonal antibody used for selection were removed using magnetic beads coated with anti-mouse immunoglobulin. 1207 EPIHRSTLTALL(1) EPIHRSTLTAPL(1) YQDMIYMRPLDS(1) PRPSPKMGVSV(1) ASNHTHSSSIQF(3) TATHRHSSSI(1) DARHSSSLQMLF(1) FSLRPTMNFTNL(1) DPGKIYFHIAVS(1) 9 Phage display (common panning) 4 PMID:10076823 Constant region of humanized anti-Tac monoclonal antibody (HAT) Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The pFc' fragments of a humanized IgG1 monoclonal antibody were generated by digestion with immobilized pepsin. These pFc' fragments were separated from F(ab')2 fragments by affinity chromatography. The pFc' fragments corresponding to the constant region of the humanized anti-Tac (HAT) IgG1 monoclonal antibody were used as targets for panning. EPIHRSTLTALL was the best peptide, which had a binding capacity of 320 mg HAT/g gel in affinity chromatography of HAT. 1208 RQLVQPL(1) SPAPSDS(1) SSQSDPA(1) SKPTQLH(1) GTATSPH(1) SHLGFDD(3) TSDTGWR(1) 7 Phage display (common panning) 4 PMID:10076823 Constant region of humanized anti-Tac monoclonal antibody (HAT) Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The pFc' fragments of a humanized IgG1 monoclonal antibody were generated by digestion with immobilized pepsin. These pFc' fragments were separated from F(ab')2 fragments by affinity chromatography. The pFc' fragments corresponding to the constant region of the humanized anti-Tac (HAT) IgG1 monoclonal antibody were used as targets for panning. 1209 RVRPAP(5) LERLPP(2) VRLPPN(9) NIRLPP(7) KIRLPP(1) ERRAPG(2) EIRRAP(1) VRYPPR(1) KSKAGV(1) R-x(2)-P 9 Phage display (common panning) 3 PMID:16695994 Anti-mucin monoclonal antibody C595 Mucin-1, MUC-1 Not determined. Not determined. f3-6mer phage display library (X6) 1210 GERWCFDGPLTWVCGEES 1 Phage display (common panning) 4 PMID:9922141 Vascular endothelial growth factor A, VEGF-A Vascular endothelial growth factor receptor 2, VEGFR-2 Not determined. Not determined. X4CX2GPX4CX4 phage display library The receptor binding domain of human VEGF (residues 8-109) was overexpressed in Escherichia coli inclusion bodies, purified, refolded and used as the target for panning. Sequencing of representitive clones yielded a single consensus sequence. Phage ELISA experiments showed that the binding of these phage clones to VEGF could be blocked by KDR. 1211 RGWVEICVADDNGMCVTEAQ GWDECDVARMWEWECFAGV 2 Phage display (common panning) 4 PMID:9922141 Vascular endothelial growth factor A, VEGF-A Vascular endothelial growth factor receptor 2, VEGFR-2 Not determined. 1IDH,1VPP, X(i)CX(j)CX(k) phage display library pool The receptor binding domain of human VEGF (residues 8-109) was overexpressed in Escherichia coli inclusion bodies, purified, refolded and used as the targetfor panning. Sequencing of representitive clones yielded two predominant sequences. Phage ELISA experiments showed that the binding of these phage clones to VEGF could be blocked by KDR. 1212 SYSWMYE(1400)[-, 0.69] YWDGQW(22)[-, 0.20] WWDGQF(13)[-, 0.17] YDWLYE(6)[-, 0.42] DYAWMY(2)[-, 0.67] 5 Phage display (common panning) 4 PMID:8760499 Anti-GXM monoclonal antibody 2H1 Glucuronoxylomannan, GXM Not determined. Not determined. f3-6mer phage display library (X6) ELISA Large-scale phage preparations were made using PEG precipitation. The direct ELISA was done by absorbing anti-phage antibody to the ELISA plate and then adding 2e10 phage. 2H1 (2 μg/ml) was then added and the ELISA was developed with an alkaline phosphatase-conjugated anti-γ1 antibody. The enhanced direct ELISA was carried out the same way with a threefold excess of anti-γ1 antibody (6 μg/ml) added together with 2H1. For the hexapeptide library, complexes between 2H1 and phage were captured with streptavidin-coated magnetic beads (Advanced Magnetics, Inc., MA). 1213 LQYTPSWMLV(18)[0.51, >2.0] NSPETPDWMV(2)[-, 0.65 ±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hage display (common panning) 4 PMID:8760499 Anti-GXM monoclonal antibody 2H1 Glucuronoxylomannan, GXM Not determined. 2H1P, L100 phage display library (X10) ELISA Large-scale phage preparations were made using PEG precipitation. The direct ELISA was done by absorbing anti-phage antibody to the ELISA plate and then adding 2e10 phage. 2H1 (2 μg/ml) was then added and the ELISA was developed with an alkaline phosphatase-conjugated anti-γ1 antibody. The enhanced direct ELISA was carried out the same way with a threefold excess of anti-γ1 antibody (6 μg/ml) added together with 2H1. For the decapeptide library, complexes between 2H1 and phage were captured with streptavidin-coated magnetic beads (Advanced Magnetics, Inc., MA) and a biotinylated anti-mouse IgG1 antibody. LQYTPSWMLV binds to 2H1 with a Kd of 295nM. The structure of GLQYTPSWMLVG complexed with 2H1 has been solved (PDB ID: 2H1P). 1214 AGRDRG[0.652] AGRDLL[1.572] RMKSSR[0.378] RLKSSR[0.988] VKKSGR[0.203] HLFEAP[0.225] HLFEAH[1.539] KQSRRG[0.379] TLDTAH[0.612] RLRVKN[0.296] DTGHHR[0.430] HRGRAQ[0.291] HRGRAA[0.343] KPDSMP[0.424] FTILRY[0.734] FFEVAH[0.513] AGRDRA[NT] AGRDRF[NT] AGRDLF[NT] AGRDSH[NT] AGRDSV[NT] RLKSMR[NT] RFKSMR[NT] VFKSAR[NT] VRKSAR[NT] IRKSSR[NT] KTSRRG[NT] KLARRG[NT] GLVEAH[NT] VLYQAH[NT] HLYSAH[NT] KLWMAH[NT] RDQHNS[NT] RDQHKS[NT] KAQEKV[NT] RAQEKV[NT] LAQDKV[NT] LAQHKS[NT] RGRLDR[NT] HHRGSA[NT] WTKQYR[NT] KNTYPI[NT] RQYRPG[NT] SQMPIF[NT] 44 Phage display (common panning) 3-4 PMID:10921846 IgG fraction of anti-EHV-1 serum Equine herpesvirus type 1 Not determined. Not determined. f3-6mer phage display library (X6) ELISA ELISA measurements of the binding to sera from EHV-1 infected gnotobiotic foals expressed as A490. The samples were taken in duplicate and the results are expressed as an average value. NT denotes not tested. Briefly phage (3e9-9e10 plaque forming units, pfu) in 100 ml PBSTG (phosphate buffered saline containing 0.05% Tween 20 and 0.5% goat sera, Seralabs) were incubated with or without biotinylated equine IgG for 5h at 37°C. An equal volume of M-280 streptavidin-coated magnetic beads (Dynal), washed three times with PBSTG, was added, mixed and stored at room temperature for 5 min. The sequences of the amino acids displayed were aligned with protein sequences of EHV-1, thereby identifying a number of potential antibody binding regions. Presumptive epitopes were identified within the proteins encoded by genes 7 (DNA helicase:primase complex protein), 11 (tegument protein), 16 (glycoprotein C), 41 (integral membrane protein), 70 (glycoprotein G), 71 (envelope glycoprotein gp300), and 74 (glycoprotein E). Two groups of sequences, which aligned with either glycoprotein C (gC) or glycoprotein E (gE), identified type-specific epitopes which could be used to distinguish between sera from horses infected with either EHV-1 or EHV-4 in an ELISA using either the phage displaying the peptide or synthetic peptides as antigen. The gC epitope had been previously identified as an immunogenic region by conventional monoclonal antibody screening whereas the gE antibody binding region had not been previously identified. 1215 KSKRGHLLL[2.870] HHRGAAPNS[2.973] PIRVPGFLG[0.110] PRLKHVQSV[0.227] SQLRTRLKG[NT] PPRVPTTLR[NT] IPPALSISQ[NT] FRRTVNNKL[NT] RLNPHHEPM[NT] ATFTKDAAT[NT] 10 Phage display (common panning) 2 PMID:10921846 IgG fraction of anti-EHV-1 serum Equine herpesvirus type 1 Not determined. Not determined. pVIII-9aa phage display library (X9) ELISA ELISA measurements of the binding to sera from EHV-1 infected gnotobiotic foals expressed as A490. The samples were taken in duplicate and the results are expressed as an average value. NT denotes not tested. Briefly phage (3e9-9e10 plaque forming units, pfu) in 100 ml PBSTG (phosphate buffered saline containing 0.05% Tween 20 and 0.5% goat sera, Seralabs) were incubated with or without biotinylated equine IgG for 5h at 37°C. An equal volume of M-280 streptavidin-coated magnetic beads (Dynal), washed three times with PBSTG, was added, mixed and stored at room temperature for 5 min. The sequences of the amino acids displayed were aligned with protein sequences of EHV-1, thereby identifying a number of potential antibody binding regions. Presumptive epitopes were identified within the proteins encoded by genes 7 (DNA helicase:primase complex protein), 11 (tegument protein), 16 (glycoprotein C), 41 (integral membrane protein), 70 (glycoprotein G), 71 (envelope glycoprotein gp300), and 74 (glycoprotein E). Two groups of sequences, which aligned with either glycoprotein C (gC) or glycoprotein E (gE), identified type-specific epitopes which could be used to distinguish between sera from horses infected with either EHV-1 or EHV-4 in an ELISA using either the phage displaying the peptide or synthetic peptides as antigen. The gC epitope had been previously identified as an immunogenic region by conventional monoclonal antibody screening whereas the gE antibody binding region had not been previously identified. 1216 YFHDRLPKPQTMKPS[0.193] TSLSWSKPPTRSSPI[0.724] LIVQDRPPSRKQHPP[0.167] MHKNNQFHWPSIRYL[0.160] MSPILDFPSRKTHKT[1.265] NSQLTKSPSMKHRVE[1.171] SLASRPHHPLKNYAP[0.113] FVAKSPAKHNPVSVR[0.148] TSMARYVRHSNYKHM[0.219] SCNDNKSVPCIVPQL[0.652] QPRLSTKKTPSSPIA[NT] LPDRPRTQPFVHELP[NT] TSLPPPRQPHPHFVP[NT] IIQYRIPHRPPTQHL[NT] KYPTPQHPTKFTQHS[NT] MPFLINRWPPVNQLL[NT] PPPRTPTQSLPMTFT[NT] SEFRHPHPHLPPFDV[NT] WHTFADMQLMYPLKE[NT] WLPKYPLESTNSLTN[NT] AGISRTAYPTRVPYT[NT] 21 Phage display (common panning) 3 PMID:10921846 IgG fraction of anti-EHV-1 serum Equine herpesvirus type 1 Not determined. Not determined. X15 M13 phage display library ELISA ELISA measurements of the binding to sera from EHV-1 infected gnotobiotic foals expressed as A490. The samples were taken in duplicate and the results are expressed as an average value. NT deneotes not tested. Briefly phage (3e9-9e10 plaque forming units, pfu) in 100 ml PBSTG (phosphate buffered saline containing 0.05% Tween 20 and 0.5% goat sera, Seralabs) were incubated with or without biotinylated equine IgG for 5h at 37°C. An equal volume of M-280 streptavidin-coated magnetic beads (Dynal), washed three times with PBSTG, was added, mixed and stored at room temperature for 5 min. The sequences of the amino acids displayed were aligned with protein sequences of EHV-1, thereby identifying a number of potential antibody binding regions. Presumptive epitopes were identified within the proteins encoded by genes 7 (DNA helicase:primase complex protein), 11 (tegument protein), 16 (glycoprotein C), 41 (integral membrane protein), 70 (glycoprotein G), 71 (envelope glycoprotein gp300), and 74 (glycoprotein E). Two groups of sequences, which aligned with either glycoprotein C (gC) or glycoprotein E (gE), identified type-specific epitopes which could be used to distinguish between sera from horses infected with either EHV-1 or EHV-4 in an ELISA using either the phage displaying the peptide or synthetic peptides as antigen. The gC epitope had been previously identified as an immunogenic region by conventional monoclonal antibody screening whereas the gE antibody binding region had not been previously identified. 1217 LPPPSYWSQ DPPSYHASS APPSYHSSV WFNPPPYPG FYWPPPYTA SMLPPPYPLP FLPPAYRKE SPPAYASSR YRPPAYANA RRPPAYPGA RPPPPYHPE NLRPPAYLQ RAPPTYERS IRSPPPYEP RPPPYARAP MRPPPYVAP RRPPAYEGWHNV HRPEPPPYGNHGH VHPPAYSYYGHE P(2)-x-Y 19 Phage display (common panning) PMID:10767429 WW-EF-ZZ fusion protein from utrophin Not determined. Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) Authors found that none of the carboxy-terminal domains of utrophin, when isolated from its structural context, selects specific ligand peptides from a phage-displayed peptide library. By contrast, panning with an extended region containing the WW, EF hands, and ZZ domain defines the consensus binding motif, PPxY which is also found in L-dystroglycan, a component of the DAP complex that interacts with utrophin in several tissues. 1218 FYPSYHSTPQRP AYYKTASLAPAE SLSLLTMPGNAS 3 Phage display (subtractive panning) 4 PMID:15187120 Human dendritic cells Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Phages were incubated serially with monocytes, T cells, and B cells, then with Langerhans-like DC, then MDC. 1219 HWKHPWGAWDTL HHWHHWCMPHKT HWSAWWIRSNQS HNWYHWWMPHNT 4 Phage display (common panning) 5 PMID:12612679 Carbon nanotubes Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Analysis of peptide conformations shows that the binding sequence is flexible and folds into a structure matching the geometry of carbon nanotubes. The hydrophobic structure of the peptide chains suggests that they act as symmetric detergents. 1220 CLYTRYWC 1 Phage display (common panning) 4 PMID:14978303 SEM-5 SH3 domain Not determined. Not determined. Not determined. CX6C FUSE5-based phage display library For library selection, streptavidin magnesphere paramagnetic particles (SA-PMPs; Promega Cat. #Z5481) were rinsed three times with Tris-buffered saline (TBS; 50 mM Tris-HCl, pH 7.5, 0.15 M NaCl). Biotinylated SH3 (100μg) was added to 0.6 mg SA-PMPs in 600 μL TBS and incubated at 4°C for 18 h. The SA-PMPs were then incubated with 10 μmole of biotin at 4°C for 4 h to block unbound sites. The library phage virions (input = e12 cfu) were added and incubated with the beads in 700 μL TBS at 4°C for 18 h. 1221 CAYTAFPLDC(13) CNTAFPSGTSC(7) 2 Phage display (common panning) PMID:12878179 Anti-mouse CD45 monoclonal antibody IBL-8 Receptor-type tyrosine-protein phosphatase C Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) Among these 20 clones we have identified two types of clones displaying slightly different nonapeptides. A comparison of the deduced amino acid sequence of these two groups of clones with the primary sequence of the CD45 molecule assigns the epitope recognised by the IBL-8 mAb to amino acids 136-144 (ADTAFPVDT). 1222 NHFLIKP(6) NHFLRSP(3) NHFLPRW(3) NHFLPKV(8) NHFLLPP(1) NHFLPPR(1) NHFLPTG(1) NHFLMPK(1) NHFLKGT(1) NHFLPQN(1) NHFLLWR(1) NHFLIRK(2) NHFLPTA(1) NHFL 13 Phage display (common panning) 4 PMID:14602648 Bacillus subtilis spores Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) 1223 NHFLKSQPGVVT(2) NHFLNRPAQSQV(1) NHFLPPKMGPTD(1) NHFLPEPRLVMP(1) NHFLAPQPPVKP(2) NHFLMPNPLLAM(1) NHFLIPPEPLRE(1) NHFLPLNPPAPS(1) NHFL 8 Phage display (common panning) 4 PMID:14602648 Bacillus subtilis spores Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) 1224 CGVVRGPSRGC(5) CALARAARLGC(1) 2 Phage display (subtractive panning) 3 PMID:12210982 Glutathione S-transferase Mu 2 Not determined. Not determined. Not determined. CX9C phage display library The library was mixed together and added to a well preblocked with nonfat dried milk in PBS. And the library was incubated for 1 hour at RT prior to transfer to GST-M2-2-coated microtiter wells. 1225 CAENRFDADLRSSALAC(1) 1 Phage display (subtractive panning) 3 PMID:12210982 Glutathione S-transferase Mu 2 Not determined. Not determined. Not determined. CX15C phage display library The library was mixed together and added to a well preblocked with nonfat dried milk in PBS. And the library was incubated for 1 hour at RT prior to transfer to GST-M2-2-coated microtiter wells.