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PubMed:1718025 JSONTXT

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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 0-26 protein denotes T-helper-cell determinants
T2 30-46 protein denotes protein antigens
T3 77-107 protein denotes cysteine-rich antigen segments
T4 145-166 protein denotes cathepsin B, L, and D
T5 240-262 protein denotes T-helper-cell epitopes
T6 266-281 protein denotes protein antigen
T7 283-285 protein denotes Ag
T8 304-306 protein denotes Ag
T9 307-326 protein denotes amino acid sequence
T10 398-400 protein denotes Ag
T11 463-484 protein denotes cathepsin B, L, and D
T12 506-513 protein denotes enzymes
T13 553-571 protein denotes soluble protein Ag
T14 578-581 protein denotes APC
T15 587-605 protein denotes resistant segments
T16 609-611 protein denotes Ag
T17 656-675 protein denotes T-cell determinants
T18 681-701 protein denotes susceptible segments
T19 790-797 protein denotes enzymes
T20 857-886 protein denotes S2, S1, S1', and S2' subsites
T21 890-907 protein denotes cathepsin B and L
T22 924-926 protein denotes S1
T23 931-934 protein denotes S1'
T24 947-958 protein denotes cathepsin D
T25 991-1030 protein denotes cysteine-containing T-cell determinants
T26 1046-1056 protein denotes protein Ag
T27 1185-1187 protein denotes Ag
T28 1324-1343 protein denotes T-cell determinants
T29 1351-1353 protein denotes Ag
T30 1470-1472 protein denotes Ag
T31 1487-1528 protein denotes amphipatic alpha-helical protein segments
T32 1579-1598 protein denotes T-cell determinants

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-167 Sentence denotes T-helper-cell determinants in protein antigens are preferentially located in cysteine-rich antigen segments resistant to proteolytic cleavage by cathepsin B, L, and D.
S2 168-327 Sentence denotes We report on a computer algorithm capable of predicting the location of T-helper-cell epitopes in protein antigen (Ag) by analysing the Ag amino acid sequence.
S3 328-485 Sentence denotes The algorithm was constructed with the aim of identifying segments in Ag which are resistant to proteolytic degradation by the enzymes cathepsin B, L, and D.
S4 486-702 Sentence denotes These are prominent enzymes in the endocytic pathway through which soluble protein Ag enter APC, and resistant segments in Ag may, therefore, be expected to contain more T-cell determinants than susceptible segments.
S5 703-959 Sentence denotes From information available in the literature on the substrate specificity of the three enzymes, it is clear that a cysteine is not accepted in any of the S2, S1, S1', and S2' subsites of cathepsin B and L, and not in the S1 and S1' subsites of cathepsin D.
S6 960-1163 Sentence denotes Moreover, we have noticed that cysteine-containing T-cell determinants in a number of protein Ag are particularly rich in the amino acids alanine, glycine, lysine, leucine, serine, threonine, and valine.
S7 1164-1415 Sentence denotes By searching protein Ag for clusters of amino acids containing cysteine and two of the other amino acids we were able to predict 17 out of 23 empirically known T-cell determinants in the Ag with a relatively low number of false (positive) predictions.
S8 1416-1529 Sentence denotes Furthermore, we present a new principle for searching Ag for potential amphipatic alpha-helical protein segments.
S9 1530-1753 Sentence denotes Such segments accord well with empirically known T-cell determinants and our algorithm produces a lower number of false positive predictions than the principle based on discrete Fourier transformations previously described.

genia-medco-coref

Id Subject Object Predicate Lexical cue
C2 38-46 NP denotes antigens
C1 30-46 NP denotes protein antigens
C4 145-159 NP denotes cathepsin B, L
C5 165-166 NP denotes D
C3 145-166 NP denotes cathepsin B, L, and D
C6 181-201 NP denotes a computer algorithm
C8 274-286 NP denotes antigen (Ag)
C7 266-286 NP denotes protein antigen (Ag)
C9 328-341 NP denotes The algorithm
C10 398-400 NP denotes Ag
C11 401-406 NP denotes which
C13 463-477 NP denotes cathepsin B, L
C12 451-484 NP denotes the enzymes cathepsin B, L, and D
C14 486-491 NP denotes These
C15 496-513 NP denotes prominent enzymes
C17 569-571 NP denotes Ag
C16 553-571 NP denotes soluble protein Ag
C18 609-611 NP denotes Ag
C19 780-797 NP denotes the three enzymes
C20 816-826 NP denotes a cysteine
C21 865-886 NP denotes S1', and S2' subsites
C22 890-907 NP denotes cathepsin B and L
C23 920-943 NP denotes the S1 and S1' subsites
C24 947-958 NP denotes cathepsin D
C26 1054-1056 NP denotes Ag
C25 1046-1056 NP denotes protein Ag
C28 1086-1097 NP denotes amino acids
C27 1082-1162 NP denotes the amino acids alanine, glycine, lysine, leucine, serine, threonine, and valine
C30 1185-1187 NP denotes Ag
C29 1177-1187 NP denotes protein Ag
C31 1204-1215 NP denotes amino acids
C32 1227-1235 NP denotes cysteine
C34 1257-1268 NP denotes amino acids
C33 1240-1268 NP denotes two of the other amino acids
C35 1347-1353 NP denotes the Ag
C36 1386-1414 NP denotes false (positive) predictions
C37 1470-1472 NP denotes Ag
C38 1477-1528 NP denotes potential amphipatic alpha-helical protein segments
C39 1530-1543 NP denotes Such segments
C40 1603-1616 NP denotes our algorithm
C41 1644-1670 NP denotes false positive predictions
R1 C8 C2 coref-ident antigen (Ag),antigens
R2 C7 C1 coref-ident protein antigen (Ag),protein antigens
R3 C9 C6 coref-ident The algorithm,a computer algorithm
R4 C10 C8 coref-ident Ag,antigen (Ag)
R5 C11 C10 coref-relat which,Ag
R6 C13 C4 coref-ident "cathepsin B, L","cathepsin B, L"
R7 C12 C3 coref-ident "the enzymes cathepsin B, L, and D","cathepsin B, L, and D"
R8 C14 C12 coref-pron These,"the enzymes cathepsin B, L, and D"
R9 C15 C12 coref-ident prominent enzymes,"the enzymes cathepsin B, L, and D"
R10 C17 C10 coref-ident Ag,Ag
R11 C16 C7 coref-ident soluble protein Ag,protein antigen (Ag)
R12 C18 C17 coref-ident Ag,Ag
R13 C19 C12 coref-ident the three enzymes,"the enzymes cathepsin B, L, and D"
R14 C22 C13 coref-ident cathepsin B and L,"cathepsin B, L"
R15 C23 C21 coref-ident the S1 and S1' subsites,"S1', and S2' subsites"
R16 C24 C5 coref-ident cathepsin D,D
R17 C26 C18 coref-ident Ag,Ag
R18 C25 C16 coref-ident protein Ag,soluble protein Ag
R19 C30 C26 coref-ident Ag,Ag
R20 C29 C25 coref-ident protein Ag,protein Ag
R21 C31 C28 coref-ident amino acids,amino acids
R22 C32 C20 coref-ident cysteine,a cysteine
R23 C34 C31 coref-ident amino acids,amino acids
R24 C33 C27 coref-other two of the other amino acids,"the amino acids alanine, glycine, lysine, leucine, serine, threonine, and valine"
R25 C35 C30 coref-ident the Ag,Ag
R26 C37 C35 coref-ident Ag,the Ag
R27 C39 C38 coref-ident Such segments,potential amphipatic alpha-helical protein segments
R28 C40 C9 coref-ident our algorithm,The algorithm
R29 C41 C36 coref-ident false positive predictions,false (positive) predictions

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 0-26 protein_domain_or_region denotes T-helper-cell determinants
T2 30-46 protein_family_or_group denotes protein antigens
T3 77-107 protein_domain_or_region denotes cysteine-rich antigen segments
T4 121-141 other_name denotes proteolytic cleavage
T5 183-201 other_name denotes computer algorithm
T6 240-262 protein_domain_or_region denotes T-helper-cell epitopes
T7 266-281 protein_family_or_group denotes protein antigen
T8 283-285 protein_family_or_group denotes Ag
T9 304-306 protein_family_or_group denotes Ag
T10 307-326 protein_domain_or_region denotes amino acid sequence
T11 398-400 protein_family_or_group denotes Ag
T12 424-447 other_name denotes proteolytic degradation
T13 506-513 protein_family_or_group denotes enzymes
T14 553-568 protein_family_or_group denotes soluble protein
T15 569-571 protein_family_or_group denotes Ag
T16 578-581 protein_complex denotes APC
T17 587-605 protein_domain_or_region denotes resistant segments
T18 609-611 protein_family_or_group denotes Ag
T19 656-675 protein_domain_or_region denotes T-cell determinants
T20 681-701 protein_domain_or_region denotes susceptible segments
T21 755-776 other_name denotes substrate specificity
T22 790-797 protein_family_or_group denotes enzymes
T23 818-826 amino_acid_monomer denotes cysteine
T24 924-926 protein_domain_or_region denotes S1
T25 931-934 protein_domain_or_region denotes S1'
T26 947-958 protein_domain_or_region denotes cathepsin D
T27 991-999 amino_acid_monomer denotes cysteine
T28 1046-1053 protein_family_or_group denotes protein
T29 1054-1056 protein_family_or_group denotes Ag
T30 1086-1097 amino_acid_monomer denotes amino acids
T31 1098-1105 amino_acid_monomer denotes alanine
T32 1107-1114 amino_acid_monomer denotes glycine
T33 1116-1122 amino_acid_monomer denotes lysine
T34 1124-1131 amino_acid_monomer denotes leucine
T35 1133-1139 amino_acid_monomer denotes serine
T36 1141-1150 amino_acid_monomer denotes threonine
T37 1156-1162 amino_acid_monomer denotes valine
T38 1185-1187 protein_family_or_group denotes Ag
T39 1204-1215 amino_acid_monomer denotes amino acids
T40 1227-1235 amino_acid_monomer denotes cysteine
T41 1257-1268 amino_acid_monomer denotes amino acids
T42 1324-1343 protein_domain_or_region denotes T-cell determinants
T43 1351-1353 protein_family_or_group denotes Ag
T44 1470-1472 protein_family_or_group denotes Ag
T45 1487-1528 protein_domain_or_region denotes amphipatic alpha-helical protein segments
T46 1579-1598 protein_domain_or_region denotes T-cell determinants
T47 1607-1616 other_name denotes algorithm
T48 1650-1670 other_name denotes positive predictions
T49 1699-1731 other_name denotes discrete Fourier transformations