1176 LPYSHKFMIHSKPTF(6) PQHYKMPVRPYSIHS(4) SSTRSLTFDFNMLHS(4) MDAQHLVALHDVAFY(4) SCCTHSTPALPQLPS(4) NAVAHQAVGPAPFLS(3) WTPSTLSHYMTSPFY(2) HLLTHKAHDNAYYAK(2) PTPCHGQVDELHAAV(1) [IL]-H-S 9 Phage display (common panning) 3 PMID:11245205 Cellulose-binding domain (CBD) Not determined. Not determined. Not determined. X15 M13 phage display library The sequence I/LHS, which was found to be an efficient binder of CBD, was fused to a synthetic gene of HRP as an affinity tag. The tagged enzyme (tHRP) was then immobilized on microcrystalline cellulose coated with CBD, thereby demonstrating the indirect immobilization of a protein to cellulose via three amino acids selected by phage display library and CBD. 1177 KLWVIPQ(3) KLWVLPK(2) KLWQVFP(1) KVWILTP(1) KVWTIPR(1) KVWYITP(1) KCCYIPT(4) KGPPITR(1) KVWDLRS(1) YVTREPR(1) K-B-W-x-B-[PTRF]-x 10 Phage display (subtractive panning) 3 PMID:12549820 DNA topoisomerase 1 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Before applying phage display library to htop(1-214) prepanning step was performed with albumin (100µg/ml) as a target. The consensus sequence identified for clones binding to the N-terminal domain was found in 35 human proteins that are either permanently or temporarily located in the nucleus. They are in majority involved in the DNA repair, transcription, RNA metabolism or cell cycle control. Four of identified proteins: Bub3 protein, Cockayne syndrome protein A, damaged DNA binding protein 2 and GRWD protein belong toWD-repeat proteins and their sequences recognized by the N-terminal domain are identically localized. 1178 LPPSIPR(11) NLRPSIP(9) LLPSIPF(7) LIPSITW(3) L-x-P-S-I-P 4 Phage display (subtractive panning) 3 PMID:12474050 Anti-JL1 leukemia-specific monoclonal antibody JL1 antigen Not determined. Not determined. Ph.D.-7 phage display library (X7) The phage library was pre-incubated with an irrelevant mAb (IgG1, kappa) for 30 min and then added into the well coated with anti-JL1 mAb. 1179 LPPSIPFGLTVG(16)[5.63] LLPSIPNQAYLG(14)[6.50] L-x-P-S-I-P 2 Phage display (subtractive panning) 3 PMID:12474050 Anti-JL1 leukemia-specific monoclonal antibody JL1 antigen Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The interaction between anti-JL1 mAb and the mimetic peptides was tested using a surface plasmon resonance biosensor. The Kd (μM) value was measured and shown. The phage library was pre-incubated with an irrelevant mAb (IgG1, kappa) for 30 min and then added into the well coated with anti-JL1 mAb. 1180 CHQKPWEC(17) 1 Phage display (subtractive panning) 2 PMID:12496764 Purified IgGs from serum of prostate cancer patient 1 Not determined. Not determined. Not determined. CX6C phage display library First, a pre-clearing step was used to remove nonspecific clones by pre-absorbing the phage peptide library onto purified IgGs from normal serum pooled from volunteer agematched blood-donor control men. Next, the pre-cleared phage library was selected onto the pool of IgGs purified from the serum of prostate cancer patients. Authors identified a consensus motif, NX[ST]DK[ST], that bound selectively to circulating antibodies from cancer patients over control antibodies from blood donors. Authors validated this motif by showing that positive serum reactivity to the peptide was specifically linked to disease progression and to shorter survival in a large patient population. 1181 CHQKPWEC(14) 1 Phage display (subtractive panning) 3 PMID:12496764 Purified IgGs from serum of prostate cancer patient 1 Not determined. Not determined. Not determined. CX6C phage display library First, a pre-clearing step was used to remove nonspecific clones by pre-absorbing the phage peptide library onto purified IgGs from normal serum pooled from volunteer agematched blood-donor control men. Next, the pre-cleared phage library was selected onto the pool of IgGs purified from the serum of prostate cancer patients. Authors identified a consensus motif, NX[ST]DK[ST], that bound selectively to circulating antibodies from cancer patients over control antibodies from blood donors. Authors validated this motif by showing that positive serum reactivity to the peptide was specifically linked to disease progression and to shorter survival in a large patient population. 1182 CKDRFERC(17) 1 Phage display (subtractive panning) 2 PMID:12496764 Purified IgGs from serum of prostate cancer patient 2 Not determined. Not determined. Not determined. CX6C phage display library First, a pre-clearing step was used to remove nonspecific clones by pre-absorbing the phage peptide library onto purified IgGs from normal serum pooled from volunteer agematched blood-donor control men. Next, the pre-cleared phage library was selected onto the pool of IgGs purified from the serum of prostate cancer patients. Authors identified a consensus motif, NX[ST]DK[ST], that bound selectively to circulating antibodies from cancer patients over control antibodies from blood donors. Authors validated this motif by showing that positive serum reactivity to the peptide was specifically linked to disease progression and to shorter survival in a large patient population. 1183 CKDRFERC(14) 1 Phage display (subtractive panning) 3 PMID:12496764 Purified IgGs from serum of prostate cancer patient 2 Not determined. Not determined. Not determined. CX6C phage display library First, a pre-clearing step was used to remove nonspecific clones by pre-absorbing the phage peptide library onto purified IgGs from normal serum pooled from volunteer agematched blood-donor control men. Next, the pre-cleared phage library was selected onto the pool of IgGs purified from the serum of prostate cancer patients. Authors identified a consensus motif, NX[ST]DK[ST], that bound selectively to circulating antibodies from cancer patients over control antibodies from blood donors. Authors validated this motif by showing that positive serum reactivity to the peptide was specifically linked to disease progression and to shorter survival in a large patient population. 1184 CNWTDKTC(4) CNITQKSC(4) CNVSDKSC(2) N-x-[ST]-D-K-[ST] 3 Phage display (subtractive panning) 2 PMID:12496764 Purified IgGs from serum of prostate cancer patient 3 Not determined. Not determined. Not determined. CX6C phage display library First, a pre-clearing step was used to remove nonspecific clones by pre-absorbing the phage peptide library onto purified IgGs from normal serum pooled from volunteer agematched blood-donor control men. Next, the pre-cleared phage library was selected onto the pool of IgGs purified from the serum of prostate cancer patients. Authors identified a consensus motif, NX[ST]DK[ST], that bound selectively to circulating antibodies from cancer patients over control antibodies from blood donors. Authors validated this motif by showing that positive serum reactivity to the peptide was specifically linked to disease progression and to shorter survival in a large patient population. 1185 CNVSDKSC(13) CNKTDKGC(2) CNWTDKTC(1) N-x-[ST]-D-K-[ST] 3 Phage display (subtractive panning) 3 PMID:12496764 Purified IgGs from serum of prostate cancer patient 3 Not determined. Not determined. Not determined. CX6C phage display library First, a pre-clearing step was used to remove nonspecific clones by pre-absorbing the phage peptide library onto purified IgGs from normal serum pooled from volunteer agematched blood-donor control men. Next, the pre-cleared phage library was selected onto the pool of IgGs purified from the serum of prostate cancer patients. Authors identified a consensus motif, NX[ST]DK[ST], that bound selectively to circulating antibodies from cancer patients over control antibodies from blood donors. Authors validated this motif by showing that positive serum reactivity to the peptide was specifically linked to disease progression and to shorter survival in a large patient population. 1186 STVPRMPLSPPN FMNPLHPRVLRP NYVIHDVPRHPA VNMGNYRQQQPL SMLDLFPRAASY SVYNVRPSSLSA TVMASPTMKSNS VNMGNYRQQQPQ KFPGPNCCHALP 9 Phage display (common panning) 5 PMID:12409405 Mycobacterium paratuberculosis Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) 1187 SLRLLQWFLWAC(6) 1 Phage display (common panning) 3 PMID:11318108 Deoxyribonuclease-2 Not determined. Not determined. Not determined. X12 phage display library One conserved sequence (SLRLLQWFLWAC) was found in six colonies, while all other sequences appeared only once. 1188 RLQAWWEMWADSYRP(5)[0.80 ± 0.03] QKRPVNISTLQELWE(3)[0.34 ± 0.02] SVQARWEAAFDLDLY(3)[0.52 ± 0.09] [LV]-Q-[AE]-x-W-E 3 Phage display (common panning) 3 PMID:12542398 Anti-human IFN-b monoclonal antibody YSB-2 Interferon beta, IFN-beta Not determined. Not determined. f3-15mer phage display library (X15) ELISA Absorbances at 450 nm was measured. Data, means ± S.D. from triplicate wells, were reproduced from the graph. Authors screened a random phage display library with a soluble form of the human type I IFN receptor (sIFNR) and a neutralizing monoclonal antibody (mAb) against IFN-b. Three clones were identified as binding YSB-2 ,but screening with sIFNR failed to identify any peptide ligands. 1189 YAPYGL(2)[88/82] WLPSSI(1)[96] RLPLGI(1)[94] QRPHAI(1)[93] KGPIHL(1)[91] FLPQGW(1)[90] LDPWSY(1)[81] LLGLRN(1)[91] QLLGFL(1)[90] AVVQHL(1)[89] NALASI(1)[88] ARLGHF(1)[85] GAVKHL(1)[81] GAARHI(1)[79] NLRSKL(1)[79] NLKSRV(1)[77] DRQMAL(1)[69] FSMFSL(1)[66] WAKSNL(1)[48] VSLKNL(1)[45] TVGWIS(1)[33] VASGIY(1)[86] PQHVRQ(1)[71] AVYFHM(1)[66] LRAMQT(1)[65] GANSLK(1)[63] RIGFLR(1)[88] VFSIPL(1)[79] RAMHMY(1)[79] RSENIR(1)[79] IKYHSL(1)[77] LISHSI(1)[73] ARYRWL(1)[72] GVSMPF(1)[67] VMSIRI(1)[61] RSYAIL(1)[55] SRRLHL(1)[50] FIANPV(1)[42] 38 Phage display (common panning) 3 PMID:11959855 Matrix metalloproteinase-14, MMP-14 Not determined. Not determined. Not determined. X6 phage display library ELISA Individual phage were analyzed after three rounds of selection by MT1-MMP. The substrates are grouped according to their ability to be hydrolyzed by MT1-MMP, relative to non-treated controls, as measured by substrate phage ELISA and expressed as % hydrolysis. Two-hundred clones were screened for their ability to be hydrolyzed by MT1-MMP using the substrate phage ELISA we reported previously. Forty of the two-hundred clones were cleaved efficiently by MT1-MMP and were carried forward for additional analysis. 1190 CPEFVDVEGDPGALLAC CGWVDVIASGDTATLAC CDVEWVDVSSLEWDLPC CLMGCWCDVGVGGESLC CPDWVDVFKLVEGVMLC [ED]-[WF]-[VC]-D-V 5 Phage display (common panning) 5-7 PMID:12393589 P-selectin P-selectin glycoprotein ligand 1 1G1S, Not determined. pComb8 CX15C phage display library In fact, chimeric P-selectin, consisting of human IgG1 fused to the binding domain of human P-selectin (PS-IgG), was the target. 1191 VGLDPRDWVDVSDYA DWVDVREVLTGEQRV DWVDV 2 Phage display (common panning) PMID:12393589 P-selectin P-selectin glycoprotein ligand 1 1G1S, Not determined. pIF4 X15 phage display library In fact, chimeric P-selectin, consisting of human IgG1 fused to the binding domain of human P-selectin (PS-IgG), was the target. 1192 ECSEGWCDMKIDRLDAGG WCDSVGDRAGPSV WCD 2 Phage display (common panning) PMID:12393589 P-selectin P-selectin glycoprotein ligand 1 1G1S, Not determined. pIF4 X28 phage display library In fact, chimeric P-selectin, consisting of human IgG1 fused to the binding domain of human P-selectin (PS-IgG), was the target. The isolated peptide sequences were not displayed completely. 1193 FLHTRLFVSDWYHTP(2) SRAPRFPWLNPLDGW(2) TFTRVVTDVYRPRLS(2) EDFRFESSLSINDHA(2) GWHTRIFVSDWYHTP(1) SLAPRFPWLNPLDGW(1) SRSPRFPWLNPLDGW(1) TFMRVVTDVYRPRLS(1) SFTRVVTDVYRPRLS(1) DFRFESSLSINDHA(1) 10 Phage display (subtractive panning) 3 PMID:12472892 Anti-L2/HNK-1 monoclonal antibody L2-412 L2/HNK-1 carbohydrate Not determined. Not determined. f3-15mer phage display library (X15) For the second and third rounds of screening, the phages were preincubated with rat IgG (100 μg/mL) to decrease non-specific binding. The phages isolated from a 15-mer peptide library by adsorption to this antibody share a consensus sequence of amino acids. The peptide mimicked several important functions of the L2/HNK-1 carbohydrate, such as binding to motor neurons in vitro, and preferential promotion of in vitro neurite outgrowth from motor axons compared with sensory neurons. 1194 VTWRMWYVPA(2) VVHMRYSFRI(5) YEIRFRYLQF(4) TGYRLVIYRL(1) ASTIRISFFV(3) AIRIVIATNI(3) SEGAVVFHAT(2) KIQLQWIVSL(2) YSGSLVLIVR(2) SHSLKLTLVI(4) MMKVVFRWSD(1) TLGGGLLLWH(1) VPVLHWTVMF(1) RVVYISAMVT(1) LVVINITYDR(1) AWTSPVDSFQ(1) YLHIVFQVPT(1) PRGYWLRIEW(1) RMRY 18 Phage display (common panning) 3 PMID:9531425 Cholesteryl ester transfer protein Cholesteryl esters, CE Not determined. Not determined. X10 phage display library Of the 36 randomly chosen clones, phage displaying VTWRMWYVPA, VVHMRYSFRI, YEIRFRYLQF and TGYRLVIYRL exhibited relatively high binding to CETP (OD450 0.4-0.7), whereas the remaining 24 clones displayed only moderate to low binding to CETP in the reported assay system. The synthesized VTWRMWYVPA inhibited CETP-catalyzed transfer of cholesteryl esters and triglycerides. Amino- and ciirboxy-terminal truncations demonstrated that the original decapeptide could be reduced to a pentapeptide without loss of either its ability to bind to CETP or its ability to inhibit CETP-mediated lipid transfer. That pentapeptide, WRMWY bound directly to CETP and its inhibition was consistent with that of a competitive inhibitor of CETP. 1195 SRPKPPNPS(15)[NT] KRGSIIPNG(5)[1.225, 1.267, 2.066] KTKKPPNPS(4)[NT] RLKPPNPTE(2)[NT] KPKTNQIRP(2)[NT] YTTTLSFQK(2)[NT] GVHRLTRPS(1)[1.035, 5.124, 0.888] GLHRSQTSM(1)[0.904, 4.587, 1.031] GRHHWASGP(1)[0.933, 5.390, 1.314] GQHKSRSFP(1)[0.976, 7.768, 0.664] RKPPNPPPP(1)[NT] KPPNPTRPE(1)[NT] KPPNPRPSL(1)[NT] RPSKPPNPV(1)[NT] KALKPPNPV(1)[NT] RRDTISPYS(1)[NT] KKTGNITPK(1)[NT] GQHHSLSTP(1)[NT] GAHASLWTP(1)[NT] GSHLSARAP(1)[NT] GMHKSVFAT(1)[NT] DTTLNYRGA(1)[NT] 22 Phage display (common panning) 1 PMID:9532590 IgG from the cerebrospinal fluid (CSF) of multiple sclerosis (MS) patients Not determined. Not determined. Not determined. pVIII-9aa phage display library (X9) ELISA Binding of the selected phagotopes to the CSF1, CSF2 and CSF3 was detected by ELISA on immobilized phage, respectively. For each sample antibody recognition of the tested phagotope and wild type phage was measured. Average values (A405nm) from two independent experiments have been determined. Results are expressed as the ratio between the average value of the tested phagotope and that of wild type phage (clone/wt A405 nm). Data shown were reproduced from the graph. NT denotes not tested. For each selection, 5 microgram of CSF IgG were immobilized using magnetic beads coated with goat anti-human IgG Fc-specific Ab. Eluted phages were subjected to immunological screening using the same CSF as probes. Positive plaques were individually picked and rescreened using CSF from MS patients and from patients affected by other neurological diseases. Fifty-seven phages positive only to the MS CSF were identified. Their sequences were mixed together in the original paper, though the two libraries were selected separately. 1196 WLQDITL(1) IDQDITV(1) QQDITVH(1) QDITLRP(1) HIRRILL(2) YPMIISP(1) ENGADVD(1) VHPPPFL(1) QDIT 8 Phage display (competitive panning) 3 PMID:9598980 Anti-syndecan-1 monoclonal antibody B-B2 Syndecan-1, SYND1 Not determined. Not determined. Ph.D.-7 phage display library (X7) B-B2 was produced by ascitic fluid and purified on a protein A column. Coated mAb was used to select the phages which were then eluted with an acidic treatment, and amplified in bacteria for the next round of selection. After the third round of selection bound phages were eluted by adding the selecting mAb as competitor. 1197 IQDITLS(1) RQDITLV(1) GHTQDIT(1) QDITLFN(4) QDITMFV(2) MQNITLF(1) QNITLSQ(1) QDIT 7 Phage display (common panning) 3 PMID:9598980 Anti-syndecan-1 monoclonal antibody B-B2 Syndecan-1, SYND1 Not determined. Not determined. Ph.D.-7 phage display library (X7) B-B2 was produced by ascitic fluid and purified on a protein A column. Coated mAb was used to select the phages which were then eluted with an acidic treatment, and amplified in bacteria for the next round of selection. After the third round of selection bound phages were eluted by adding the selecting mAb as competitor and then acidic conditions were applied to recover the remaining phages. Independently of the elution procedure used, the number of recovered phages was at least 30 times higher from the well coated with the selecting mAb than with an irrelevant control mAb, suggestting that the selected phages were mAb specific. 1198 LTLPEVA(1) APLPEVL(1) HLPEVSP(1) FLPEVLL(1) YLPEVIS(1) YLPEVLP(1) YLPEVQP(2) FLPDVAS(1) FLPDVLS(1) YLPQVAS(1) LTDVRTP(1) TTNDFTR(1) LPEV 12 Phage display (competitive panning) 3 PMID:9598980 Anti-syndecan-1 monoclonal antibody B-B4 Syndecan-1, SYND1 Not determined. Not determined. Ph.D.-7 phage display library (X7) B-B4 was produced by ascitic fluid and purified on a protein A column. Coated mAb was used to select the phages which were then eluted with an acidic treatment, and amplified in bacteria for the next round of selection. After the third round of selection bound phages were eluted by adding the selecting mAb as competitor. 1199 ILPEVVS(1) TLPEVLS(1) QLPEVSS(1) ALPEVLS(1) MLPEVLP(1) LELPEVM(1) VLQEVSS(1) AFPSPTL(1) AYTSAHK(1) LPEV 9 Phage display (common panning) 3 PMID:9598980 Anti-syndecan-1 monoclonal antibody B-B4 Syndecan-1, SYND1 Not determined. Not determined. Ph.D.-7 phage display library (X7) B-B4 was produced by ascitic fluid and purified on a protein A column. Coated mAb was used to select the phages which were then eluted with an acidic treatment, and amplified in bacteria for the next round of selection. After the third round of selection bound phages were eluted by adding the selecting mAb as competitor and then acidic conditions were applied to recover the remaining phages. Independently of the elution procedure used, the number of recovered phages was at least 30 times higher from the well coated with the selecting mAb than with an irrelevant control mAb, suggestting that the selected phages were mAb specific. 1200 WWIWWPGSVE(4) WWGPVIMWDA(2) WFSWGFPQWW(1) VWWSLLVPLA(4) SWGFPVFWHR(1) STGFPIFWHS(1) PEGEYAWWVE(1) DWWSYAWTLV(1) WLWVSRWPGG(2) WWLLWTIPSW(1) GMWWWPLFTL(1) PQVWGVWTDE(1) VLNWPGMLLV(1) WHLACAGVFS(1) WWTLIYLMP(1) 15 Phage display (common panning) 3 PMID:9661811 MDDQRDLISNNEQLK peptide Not determined. Not determined. Not determined. fUSE5-based X10 phage display library When screening a large number of individual phage clones for binding to biotinylated Ii peptide (MDDQRDLISNNEQLK) coupled to microtiter wells, seven phage clones binding significantly above background level were identified. Sequencing of phage inserts revealed that one displayed WFSWGFPQWW, two had insert WWGPVIMWDA, and four contained WWIWWPGSVE.