1326 HEIGSLAGLAMR(1) AHFNGSLRSLTQ(1) IINTGSLLSLAH(1) DTGSLVWLSQRS(1) HNHGSISALMHL(1) DHDRLIRRTAQI(1) FHTLDNNIRNVN(1) FHDTSLLSHHLA(1) G-S-L-x(2)-L 8 Phage display (common panning) 4 PMID:20961714 Anti-FMDV Asia1 antigen monoclonal antibody 3E11 Polyprotein Not determined. Not determined. Ph.D.-12 phage display library (X12) Through a 12-mer random peptide phage display, synthetic peptide analysis and constructing a series of FMDV Asia1/YS/CHA/05 mutants using reverse genetic system, we finely mapped the neutralizing epitope as the 12-amino acid peptide 141SXRGXLXXLXRR152. 1327 ELKQSAQVQAKI HLWSFALPSAQV INSARIMPPNWR TSPQARLEAIEP YSLRQDYNPEPV YSLRQDVLVLEE YSLRNDWPTLPP SLTNSMFPGYAY HMSIWPERWPLS HSLRPEWRMPGP FQIAPTDPASNA SPKIISSGLPTY TSSGLAPTPIMQ FGTGLASHSPAW HNLVPRHLGTVL SYQWHHLGTWLT STYGSHLGWGHF GIHLNFKVTHMH WHSTMSWTNSTW AGHDRLAVTPSS LTRSLDSHSMNT 21 Phage display (common panning) 3 PMID:21071249 Methylmalonic aciduria and homocystinuria type C protein Methylmalonic aciduria and homocystinuria type D protein, mitochondrial Not determined. Not determined. Ph.D.-12 phage display library (X12) The MMACHC-affinity-selected peptides were scanned against MMADHC to predict binding sites of MMACHC on this protein. Five distinct regions of multiply-aligning clusters were located along the primary sequence of MMADHC. Two regions were positioned in a domain with homology to ATPase component of a bacterial ATP-binding cassette (ABC) transporter: Region I, residues142-150; and Region II, residues 157-169. The other three regions were located in the C-terminal domain of MMADHC: Region III, residues 220-236; Region IV, residues 246-256; and Region V, residues 280-290. 1328 LLDSARH GPASGPM TPSSNRF AHTPNSR 4 Phage display (common panning) 3 PMID:21071249 Methylmalonic aciduria and homocystinuria type C protein Methylmalonic aciduria and homocystinuria type D protein, mitochondrial Not determined. Not determined. Ph.D.-7 phage display library (X7) The MMACHC-affinity-selected peptides were scanned against MMADHC to predict binding sites of MMACHC on this protein. Five distinct regions of multiply-aligning clusters were located along the primary sequence of MMADHC. Two regions were positioned in a domain with homology to ATPase component of a bacterial ATP-binding cassette (ABC) transporter: Region I, residues142-150; and Region II, residues 157-169. The other three regions were located in the C-terminal domain of MMADHC: Region III, residues 220-236; Region IV, residues 246-256; and Region V, residues 280-290. 1329 NMNKHPLAYTEP(1) FHWSWYTPSRPS(5) WHFEWWRATPSG(1) VLPPKPMRQPVA(1) HLQSMKPRTHVL(1) 5 Phage display (common panning) 4 PMID:21214859 Glutathione S-transferase, GST Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) 1330 CHLYTAGSCNMS(2) CHLSATGACRMI(5) IGSDMKGMPKPR(1) KSLSRHDHIHHH(1) 4 Phage display (common panning) 4 PMID:21214859 Cytoplasmic domain of CORYNE Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) In fact, the target is recombinant glutathione S-transferase(GST)-CRN-His6. Two positive clones that specifically bind to the intracellular protein kinase domain of CRN, CHLYTAGSCNMS and CHLSATGACRMI, have been identified. Alignment of these peptides and the kinase-associated protein phosphatase (KAPP) shows high similarity, indicating that KAPP might interact with the cytoplasmic kinase domain of CRN and negatively regulate the CLV signal. 1331 SYTFHWHQSWSS(3) QSWSWHWTSHVT(3) WTWRWAHVTNTR(1) QDVHLTQQSRYT(1) HKAHEYDPWISP(1) SYSQHYGIPNPW(1) SSWQMSWSWMGS(1) QSWS 7 Phage display (common panning) 5 PMID:21259034 Dry degummed silk fibroin fibers Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The selected silk-binding peptides contained a consensus sequence QSWS which is important for silk-binding as confirmed by binding assays using phage and synthetic peptides. 1332 EHYLDKWASHDM(1) LPQLNTLDKWAT(2) ASSLDKWALYTS(2) AAMTNHVLDKWA(1) YKLDKWAPSLSK(1) YPTLDKWAMWMH(1) KHLALDKWSILA(1) LPHLDKWSSITP(1) ITPALDKWSTRF(1) QVPLDKWSVAWP(1) MDLDKWNMKSLT(1) SLDKWVLAPLAY(1) NGLDISLDKWGV(1) HPLTLLDKWTLL(1) QSHYDKWASWGF(1) ALSEDKWASTAS(1) YGFPYDKWASRP(1) NMDKWAAVFQSK(2) YLPDKWATPQMI(1) ATNYDKWALPYT(1) EHAYDKWAQRXX(1) TPDKWALPHPTL(1) QFIPDKWARSPN(1) AIQLVYDKWAMP(1) HLPYTSDKWALM(1) YMDKWANIVALR(1) SHPGPDKWQTLP(2) TPDKWYGLAPYR(2) TPDLWSYLSNLQ(1) TNLFDKWSYLAS(1) YPNIDKWVALYH(1) ANDPDKWNLTPL(1) SPIHDKWSDLSR(1) TPFLDKWVALKP(1) YLPTDKWSHLRT(1) SWPFDKWSQSLS(1) SLHETHMLDRWA(1) TTLQTLDRWSQL(2) LESSLDRWTTLA(2) QTMDRWASLRWS(1) LVPDRWAFLQMS(2) MPDPDRWALWPL(1) ALVSDRWSWMHQ(1) ETLAKDRWVTLG(1) DPWAFRWPSGPM(1) ELDKWAS 45 Phage display (common panning) 3 PMID:21237206 Anti-HIV-1 gp41 MPER monoclonal antibody 2F5 HIV-1 gp41 membrane proximal exterior region (MPER) Not determined. Not determined. Ph.D.-12 phage display library (X12) 1333 CKTLDKWAC(4) CMALDKWAC(2) CWHLDKWAC(2) CWTLDKWAC(1) CLVLDKWAC(1) CLRLDKWAC(1) CVSLDKWAC(1) CLGNDKWAC(1) CDKWAPPTC(5) CDKWAGLLC(4) CDKWAPTSC(3) CDKWALAYC(2) CDKWAPRSC(1) CDKWAVRWC(1) CDKWAPPSC(1) CDKWAEQYC(1) CDKWASQPC(1) CDKWAFMTC(1) CDKWAPPGC(1) CDKWAPSAC(1) CDKWAPSWC(1) CDKWAQTYC(1) CDKWATRFC(1) CDKWAGRAC(1) CDKWAGPRC(1) CDKWAPRQC(1) CDKWAIPWC(1) LDKWA 27 Phage display (common panning) 3 PMID:21237206 Anti-HIV-1 gp41 MPER monoclonal antibody 2F5 HIV-1 gp41 membrane proximal exterior region (MPER) Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) 1334 SNFFDRTWPKLT YNFFDRTWPKLT SHRQHETDRNWP NYPEDFFQRTWP F(2)-D-R-T-W-P 4 Phage display (common panning) 3 PMID:21264311 Anti-DENV2 monoclonal antibody 2A10G6 Dengue virus 2, DENV2 Not determined. Not determined. Ph.D.-12 phage display library (X12) After three rounds of panning, 94 positive phage clones were identified and subjected to DNA sequence analysis. The results showed that 86 of the positive clones displayed 12 amino acid residues in common, i.e., SNFFDRTWPKLT. Phage-display biopanning and structure modeling mapped 2A10G6 to a new epitope within the highly conserved flavivirus fusion loop peptide, the 98DRXW101 motif. 1335 APRDPLS(1) DPFFYTP(1) GLDHHPP(1) GYDKHPQ(1) HFTNHPQ(2) HLANHPQ(1) HLENHPM(2) HLIAHPQ(1) HLYAHPQ(2) HRISWPS(1) HYEGHPQ(1) IAPNHPQ(2) IPEWHPQ(8) IPYWHPQ(3) ISSTHPQ(1) MQSHQDS(1) NLISHPQ(1) NLLNHPQ(11) NLVNHPQ(4) NLVSHPQ(1) NPTKHQM(1) PLLAHPQ(1) SLIAHPQ(4) SLLAHPH(1) SLLAHPQ(7) SLLSHPQ(2) SLVSHPM(1) SPTYQRL(1) TLIAHPQ(1) TLISHPQ(5) TLLAHPQ(8) TLLNHPQ(2) TLQPGGA(1) TPSPLAG(1) VTPTMHP(1) YLVNHPQ(1) YMEHSRV(1) HPQ 37 Phage display (common panning) 4 PMID:21278676 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. Ph.D.-7 phage display library (X7) One hundred phage isolates were sequenced after the fourth round of selection against streptavidin-coated beads. 1336 HHHPPLA(5) HHPPFPP(2) HPPSWGD(2) HPPHFPN(1) HPTGLFR(2) HNHLGVH(2) KPFHNST(5) KPGYSSA(2) KPPQVPL(2) KPHAPHR(1) KPPHHPR(3) KPPHPVY(1) KPVKVPR(2) 13 Phage display (common panning) 4 PMID:21278676 Unmodified helix 31 of bacterial 16S ribosomal RNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Duplicate samples of unmodified h31 on magnetic beads were employed for selection. For each sample of unmodified h31, 100 isolates were sequenced. Two hundred phage isolates were sequenced after the fourth round of selection against unmodified h31 on streptavidin-coated beads. Two hundred phage isolates were sequenced after the fourth round of selection against unmodified h31 on streptavidin-coated beads. Only peptides with repeated sequences or common motifs are shown. 1337 FVRPFPL(6) FVRPFAL(4) FVRPYAP(2) FPRTIAP(1) DIRTQRE(4) DIRTQTR(2) DIRATQA(2) ATPLWLK(5) ATPTQRE(3) ATPLYLR(2) TLWDLIP(5) TLWSFMP(3) TLWVPSR(2) TLTTLTN(2) TLTFFHR(2) TYLPWPA(5) TYLPWPP(2) TYLRARL(3) TYPFAPW(2) TLW, VRP 19 Phage display (common panning) 3 PMID:21278676 Modified helix 31 of bacterial 16S ribosomal RNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Duplicate samples of h31 on magnetic beads were employed for selection. For each sample of h31, 100 isolates were sequenced. Phage isolates were sequenced after the third round of selection against wild-type modified h31 on streptavidin-coated beads. Two hundred phage isolates were sequenced after the third round of selection against wild-type modified h31 on streptavidin-coated beads. Only peptide sequences with repeated sequences or common motifs are shown. Several of the peptides exhibited moderate affinity (in the high nM to low μM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays. 1338 CVRPFAL(5) CVRAPTL(2) TVRPFTL(2) TLWDLIP(2) TLWPLSP(2) TLW, VRP 5 Phage display (subtractive panning) 3 PMID:21278676 Modified helix 31 of bacterial 16S ribosomal RNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) A separate counter selection was also carried out in the third round of selection against wild-type h31 in which free unmodified h31 was added to the phage and modified h31-streptavidin mixture. One hundred phage isolates were sequenced after the third round of selection. Only peptide sequences with repeated sequences or common motifs are shown. Several of the peptides exhibited moderate affinity (in the high nM to low μM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays. 1339 SDSLMKKPGGPG(1) MYHHRKKPGGPG(1) MGAMHKKPGKTG(1) VHKYDKKRGKRG(1) PTGKMKKAGGLL(1) EPPRYKKHGGAS(1) AHHTLLELWTQA(1) ASYSNLTHWLSS(1) SPRLTTYKASPK(1) DMHHKPGRTLHH(1) K(2)-P-G(2)-P-G 10 Phage display (common panning) 3 PMID:21375771 Anti-WNV C protein monoclonal antibody 6D3 Capsid protein C Not determined. Not determined. Ph.D.-12 phage display library (X12) The mAb 6D3 recognized the phages displaying a consensus motif consisting of the amino acid sequence KKPGGPG, which is identical to an amino acid sequence present in WNV C protein. Further fine mapping was conducted using truncated peptides expressed as MBP-fusion proteins. 1340 AYYPQNHKSNAE 1 Phage display (common panning) 5 PMID:21329494 Bovine serum albumin (BSA) Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) 1341 WHWRNPDFWYLK(0.225) WHWTWLSEYPPP(0.215) LETSKLPPPAFL(0.125) WHWSQWLSGSPP(0.085) WHRTPQFWAFPW(0.07) SVSVGMKPSPRP(0.05) WHKTPWFWPTNL(0.05) WHWSWQPQRHSP(0.04) WHWQYTPWWRGS(0.03) 9 Phage display (common panning) 5 PMID:21329494 Gliadin Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Panning was done both with gliadin dissolved in urea and in NaHCO 3. Since electrostatic binding of the phage to the target protein weakens with increasing ionic strength, which in turn influences the specificity of the interaction, different buffers with different ionic strengths were tested prior the actual panning experiments. Although identical sequences were frequently picked up in independent experiments, altogether more than 160 unique sequences encoding peptides with potential gliadin binding activities were identified. In order to confirm that the selected phage clones interacted with gliadin proteins, nine different phage populations that had repeatedly been picked up in different panning experiments were chosen. Together, these nine sequences represent 89% of all identified gliadin-binding sequences. 1342 HAPVQPN(1) CTGPTSLSC(2) CKPMQFVHC(1) CSSYEYHAC(1) CSTQAHPWC(1) CGTSRLFSC(1) CASHNPKLC(1) CPAKQKAHC(2) CSASGTPSC(1) CTRFYRPSC(1) CQNPRQIYC(4) CNPQMQRSC(5) CNYPTLKSC(7) NPYHPTIPQSVH(4) HQFISPEPFLIS(1) SPNFSWLPLGTT(2) SVSVGMKPSPRP(2) TPLTSPSLVRPQ(1) 18 Phage display (competitive panning) 4 PMID:21291244 Single-crystal hydroxyapatite (HAP) Not determined. Not determined. Not determined. Ph.D.-12, Ph.D.-7 and Ph.D.-C7C phage display library pool In last round, the HAP binding phages were simultaneously exposed to the HAP target substrate in solution. 1343 CNERQMELC(1) CNKPLSTLC(1) CHTLLSTTC(1) CLKPFSGAC(1) CLGPGKAFC(4) CSTSAKHWC(1) TMGFTAPRFPHY(7) 7 Phage display (competitive panning) 4 PMID:21291244 Polycrystalline hydroxyapatite (HAP) Not determined. Not determined. Not determined. Ph.D.-12, Ph.D.-7 and Ph.D.-C7C phage display library pool In last round, the HAP binding phages were simultaneously exposed to the HAP target substrate in solution. 1344 HWKHLHNTKTFL 1 Phage display (common panning) 4 PMID:21295090 Amino acid (160)REVPYAYIREGHEKQ(174) of MMP-14 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Peptide HWKHLHNTKTFL (denoted as MT1-AF7p) showed high MT1-MMP binding affinity. Computer modeling verified that MT1-AF7p binds to the MT-loop region of MT1-MMP and interacts with MT1-MMP through hydrogen bonding and hydrophobic interactions. 1345 TYTDWLNFWAWP(1) 1 Phage display (common panning) 5 PMID:21297616 Myelin basic protein, MBP Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) In the selection against MBP, phage expressing a library of peptides were selected through multiple cycles for binding to biotinylated MBP, using avidin agarose to isolate selected phage. Specifically, the phage library was mixed with biotinylated MBP and allowed to bind for 1 h. Avidin agarose was added and incubated for an additional hour. Nonbinding phage were removed by washing the agarose three times with PBS solution and the supernatant was plated for titer and amplification for subsequent cycles. 1346 NTQTLAKAPEHT(5) KSLSRHDHIHHH(2) DFTKTSPLGIH(2) 3 Phage display (subtractive panning) PMID:21297616 Excised murine peripheral nerves Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Specifically, for positive selection using nerve tissue, nerve tissue was dissected/washed and mixed with a phage library. For negative selection using nonnerve tissues, nonnerve tissues (muscle and fat) were dissected from normal mice and incubated with the phage library obtained from the positive selection. 1347 AHHNSWKAKHHS(1) 1 Phage display (in vivo) 8 PMID:21297616 Nerve tissue (sciatic, brachial plexus, cranial nerves) Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) 1348 CSTSMLKAC(79) CKPGTSSYC(20) CPDRSVNNC(18) 3 Phage display (in vivo) 3 PMID:21316369 Ischemic region of left ventricular (LV) Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The CSTSMLKAC sequence was capable of mediating selective homing of phage to ischemic heart tissue. 1349 CWEPMNHLC(14) CPFASYLHC(13) CENVWYPRC(9) 3 Phage display (in vivo) 3 PMID:21316369 Non-ischemic region of left ventricular (LV) Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The first two rounds of bio-panning were performed against ischemic left ventricular (LV) tissue. 1350 CQSTMSTLC(13) CPTSFLTDC(9) CYDLRSHQC(7) 3 Phage display (in vivo) 3 PMID:21316369 Right ventricular (RV) Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The first two rounds of bio-panning were performed against ischemic left ventricular (LV) tissue.