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●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP
Download all results in tab-seperated text for 45686 receptor-ligand interactions, whose format is explained at readme.txt.
  • Hover over PDB to view the title of the structure. Click PDB to view the structure at the RCSB PDB database. Resolution -1.00 means the resolution is unavailable, e.g., for NMR structures.
  • Click Site # to view the binding site structure. Hover over Site # to view the binding residues.
  • The sequence is converted from residues with experimentally determined coordinates in the structure; residues not observed in the 3D structure are excluded.
  • Hover over EC number to view the full name of enzymatic activity.
  • Hover over GO terms to view all GO terms.
  • Hover over UniProt to view the protein name.

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    # PDB
    (resolution)     		Site
    #     		DNA
    sequence         		EC
    number     		GO
    terms     		UniProt PubMed Binding
    affinity
    801 1hcq:E
    (2.4)    		 BS02 >1hcq:H (identical to 1hcq:D)
    ccaggtcactgtgacctg
    		 ? GO:0003700 ... P03372 8221895
    802 1hcq:F
    (2.4)    		 BS01 >1hcq:G (identical to 1hcq:C)
    ccaggtcacagtgacctg
    		 ? GO:0003700 ... P03372 8221895
    803 1hcq:F
    (2.4)    		 BS02 >1hcq:H (identical to 1hcq:D)
    ccaggtcactgtgacctg
    		 ? GO:0003700 ... P03372 8221895
    804 1hcr:A
    (2.3)    		 BS01 >1hcr:B (identical to 1ijw:A)
    tgtttttgataaga
    		 ? GO:0000150 ... P03013 8278807
    805 1hcr:A
    (2.3)    		 BS02 >1hcr:C
    tcttatcaaaaac
    		 ? GO:0000150 ... P03013 8278807
    806 1hdd:C
    (2.8)    		 BS01 >1hdd:A (identical to 1du0:C, 3hdd:C)
    ttttgccatgtaattacctaa
    		 ? GO:0000981 ... P02836 1977522
    807 1hdd:C
    (2.8)    		 BS02 >1hdd:B (identical to 1du0:D, 3hdd:D)
    attaggtaattacatggcaaa
    		 ? GO:0000981 ... P02836 1977522
    808 1hdd:D
    (2.8)    		 BS01 >1hdd:A (identical to 1du0:C, 3hdd:C)
    ttttgccatgtaattacctaa
    		 ? GO:0000981 ... P02836 1977522
    809 1hdd:D
    (2.8)    		 BS02 >1hdd:B (identical to 1du0:D, 3hdd:D)
    attaggtaattacatggcaaa
    		 ? GO:0000981 ... P02836 1977522
    810 1hf0:A
    (2.7)    		 BS01 >1hf0:M
    cacatttgaaaggcaaatggag
    		 ? GO:0000981 ... P14859 11583619
    811 1hf0:A
    (2.7)    		 BS02 >1hf0:N
    ctccatttgcctttcaaatgtg
    		 ? GO:0000981 ... P14859 11583619
    812 1hf0:B
    (2.7)    		 BS01 >1hf0:M
    cacatttgaaaggcaaatggag
    		 ? GO:0000981 ... P14859 11583619
    813 1hf0:B
    (2.7)    		 BS02 >1hf0:N
    ctccatttgcctttcaaatgtg
    		 ? GO:0000981 ... P14859 11583619
    814 1hht:P
    (2.9)    		 BS01 >1hht:D (identical to 1hht:E, 1hht:F, 2jlg:D, 2jlg:E)
    tttcc
    		 2.7.7.48 GO:0000166 ... P11124 11242087
    815 1hht:Q
    (2.9)    		 BS01 >1hht:E (identical to 1hht:D, 1hht:F, 2jlg:D, 2jlg:E)
    tttcc
    		 2.7.7.48 GO:0000166 ... P11124 11242087
    816 1hht:R
    (2.9)    		 BS01 >1hht:F (identical to 1hht:D, 1hht:E, 2jlg:D, 2jlg:E)
    tttcc
    		 2.7.7.48 GO:0000166 ... P11124 11242087
    817 1hi0:P
    (3.0)    		 BS01 >1hi0:D (identical to 1hi0:E, 1hi0:F, 2jlg:F)
    ttcc
    		 2.7.7.48 GO:0000166 ... P11124 11242087
    818 1hi0:Q
    (3.0)    		 BS01 >1hi0:E (identical to 1hi0:D, 1hi0:F, 2jlg:F)
    ttcc
    		 2.7.7.48 GO:0000166 ... P11124 11242087
    819 1hi0:R
    (3.0)    		 BS01 >1hi0:F (identical to 1hi0:D, 1hi0:E, 2jlg:F)
    ttcc
    		 2.7.7.48 GO:0000166 ... P11124 11242087
    820 1hjb:A
    (3.0)    		 BS01 >1hjb:G (identical to 1hjb:I, 1io4:E)
    gaagatttccaaactctgtggttgcg
    		 ? GO:0003700 ... P17676 11257229
    821 1hjb:A
    (3.0)    		 BS02 >1hjb:H (identical to 1hjb:J, 1io4:F)
    ccgcaaccacagagtttggaaatctt
    		 ? GO:0003700 ... P17676 11257229
    822 1hjb:B
    (3.0)    		 BS01 >1hjb:G (identical to 1hjb:I, 1io4:E)
    gaagatttccaaactctgtggttgcg
    		 ? GO:0003700 ... P17676 11257229
    823 1hjb:B
    (3.0)    		 BS02 >1hjb:H (identical to 1hjb:J, 1io4:F)
    ccgcaaccacagagtttggaaatctt
    		 ? GO:0003700 ... P17676 11257229
    824 1hjb:C
    (3.0)    		 BS01 >1hjb:G (identical to 1hjb:I, 1io4:E)
    gaagatttccaaactctgtggttgcg
    		 ? GO:0003677 ... Q03347 11257229
    825 1hjb:C
    (3.0)    		 BS02 >1hjb:H (identical to 1hjb:J, 1io4:F)
    ccgcaaccacagagtttggaaatctt
    		 ? GO:0003677 ... Q03347 11257229
    826 1hjb:D
    (3.0)    		 BS01 >1hjb:I (identical to 1hjb:G, 1io4:E)
    gaagatttccaaactctgtggttgcg
    		 ? GO:0003700 ... P17676 11257229
    827 1hjb:D
    (3.0)    		 BS02 >1hjb:J (identical to 1hjb:H, 1io4:F)
    ccgcaaccacagagtttggaaatctt
    		 ? GO:0003700 ... P17676 11257229
    828 1hjb:E
    (3.0)    		 BS01 >1hjb:I (identical to 1hjb:G, 1io4:E)
    gaagatttccaaactctgtggttgcg
    		 ? GO:0003700 ... P17676 11257229
    829 1hjb:E
    (3.0)    		 BS02 >1hjb:J (identical to 1hjb:H, 1io4:F)
    ccgcaaccacagagtttggaaatctt
    		 ? GO:0003700 ... P17676 11257229
    830 1hjb:F
    (3.0)    		 BS01 >1hjb:I (identical to 1hjb:G, 1io4:E)
    gaagatttccaaactctgtggttgcg
    		 ? GO:0003677 ... Q03347 11257229
    831 1hjb:F
    (3.0)    		 BS02 >1hjb:J (identical to 1hjb:H, 1io4:F)
    ccgcaaccacagagtttggaaatctt
    		 ? GO:0003677 ... Q03347 11257229
    832 1hjc:A
    (2.65)    		 BS01 >1hjc:B (identical to 1hjc:E)
    gaactctgtggttgcg
    		 ? GO:0003677 ... Q03347 11257229
    833 1hjc:A
    (2.65)    		 BS02 >1hjc:C (identical to 1hjc:F)
    ccgcaaccacagagtt
    		 ? GO:0003677 ... Q03347 11257229
    834 1hjc:D
    (2.65)    		 BS01 >1hjc:E (identical to 1hjc:B)
    gaactctgtggttgcg
    		 ? GO:0003677 ... Q03347 11257229
    835 1hjc:D
    (2.65)    		 BS02 >1hjc:F (identical to 1hjc:C)
    ccgcaaccacagagtt
    		 ? GO:0003677 ... Q03347 11257229
    836 1hlo:A
    (2.8)    		 BS01 >1hlo:C
    caccacgtggt
    		 ? GO:0046983 ... P61244 9115440
    837 1hlo:A
    (2.8)    		 BS02 >1hlo:D
    accacgtggtg
    		 ? GO:0046983 ... P61244 9115440
    838 1hlo:B
    (2.8)    		 BS01 >1hlo:C
    caccacgtggt
    		 ? GO:0046983 ... P61244 9115440
    839 1hlo:B
    (2.8)    		 BS02 >1hlo:D
    accacgtggtg
    		 ? GO:0046983 ... P61244 9115440
    840 1hlv:A
    (2.5)    		 BS01 >1hlv:B
    gccttcgttggaaacgggatt
    		 ? GO:0003677 ... P07199 11726497
    841 1hlv:A
    (2.5)    		 BS02 >1hlv:C
    aatcccgtttccaacgaaggc
    		 ? GO:0003677 ... P07199 11726497
    842 1hlz:A
    (2.8)    		 BS01 >1hlz:C (identical to 1ga5:C, 1ga5:G)
    caactaggtcactaggtcag
    		 ? GO:0003700 ... P20393 11669620
    843 1hlz:A
    (2.8)    		 BS02 >1hlz:D (identical to 1a6y:D)
    ctgacctagtgacctagttg
    		 ? GO:0003700 ... P20393 11669620
    844 1hlz:B
    (2.8)    		 BS01 >1hlz:C (identical to 1ga5:C, 1ga5:G)
    caactaggtcactaggtcag
    		 ? GO:0003700 ... P20393 11669620
    845 1hlz:B
    (2.8)    		 BS02 >1hlz:D (identical to 1a6y:D)
    ctgacctagtgacctagttg
    		 ? GO:0003700 ... P20393 11669620
    846 1hry:A
    (-1.00)    		 BS01 >1hry:B (identical to 1hrz:B)
    gcacaaac
    		 ? N/A Q05066 7774012
    847 1hry:A
    (-1.00)    		 BS02 >1hry:C (identical to 1hrz:C)
    gtttgtgc
    		 ? N/A Q05066 7774012
    848 1hrz:A
    (-1.00)    		 BS01 >1hrz:B (identical to 1hry:B)
    gcacaaac
    		 ? N/A Q05066 7774012
    849 1hrz:A
    (-1.00)    		 BS02 >1hrz:C (identical to 1hry:C)
    gtttgtgc
    		 ? N/A Q05066 7774012
    850 1hu0:A
    (2.35)    		 BS01 >1hu0:D (identical to 1ebm:D, 4ejy:D, 4ejy:F, 1fn7:C, 1lwv:D, 1lww:D, 1lwy:D, 1m3h:B, 1m3q:B, 1n39:B, 1n3a:B, 1n3c:B, 2noh:B, 2nol:B, 6w0m:C)
    ggtagacctggacgc
    		 3.2.2.-
    4.2.99.18    		 GO:0000978 ... O15527 12592398
    851 1hu0:A
    (2.35)    		 BS02 >1hu0:E (identical to 1fn7:D, 1lwv:E, 1lww:E, 1lwy:E, 1m3q:C, 1n39:C, 1n3a:C)
    gcgtccacgtctacc
    		 3.2.2.-
    4.2.99.18    		 GO:0000978 ... O15527 12592398
    852 1huo:A
    (2.6)    		 BS01 >1huo:T (identical to 1huo:C, 1huz:T, 1huz:C)
    aggcgtcg
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    853 1huo:A
    (2.6)    		 BS02 >1huo:P (identical to 1huo:D)
    cgacgcc
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    854 1huo:B
    (2.6)    		 BS01 >1huo:C (identical to 1huo:T, 1huz:T, 1huz:C)
    aggcgtcg
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    855 1huo:B
    (2.6)    		 BS02 >1huo:D (identical to 1huo:P)
    cgacgcc
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    856 1hut:H
    (2.9)    		 BS01 >1hut:D (identical to 4dih:D, 4dii:D, 6eo6:D, 6eo7:D, 1hao:D, 1hap:D, 3qlp:D, 6z8v:A, 6z8w:A, 7zkl:A, 7zkm:B, 7zkn:E)
    ggttggtgtggttgg
    		 3.4.21.5 GO:0004252 ... P00734 8102368
    857 1huz:A
    (2.6)    		 BS01 >1huz:T (identical to 1huo:T, 1huo:C, 1huz:C)
    aggcgtcg
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    858 1huz:A
    (2.6)    		 BS02 >1huz:P (identical to 1huz:D)
    cgacgcct
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    859 1huz:B
    (2.6)    		 BS01 >1huz:C (identical to 1huo:T, 1huo:C, 1huz:T)
    aggcgtcg
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    860 1huz:B
    (2.6)    		 BS02 >1huz:D (identical to 1huz:P)
    cgacgcct
    		 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06766 11330999
    861 1hw2:A
    (3.25)    		 BS01 >1hw2:D
    cgatctggtccgaccagatg
    		 ? GO:0000062 ... P0A8V6 11279025
    862 1hw2:A
    (3.25)    		 BS02 >1hw2:E
    catctggtcggaccagat
    		 ? GO:0000062 ... P0A8V6 11279025
    863 1hw2:B
    (3.25)    		 BS01 >1hw2:D
    cgatctggtccgaccagatg
    		 ? GO:0000062 ... P0A8V6 11279025
    864 1hw2:B
    (3.25)    		 BS02 >1hw2:E
    catctggtcggaccagat
    		 ? GO:0000062 ... P0A8V6 11279025
    865 1hwt:C
    (2.5)    		 BS01 >1hwt:A (identical to 1hwt:E)
    gcgctattatcgctattagc
    		 ? GO:0000981 ... P0CS82 9886294
    866 1hwt:C
    (2.5)    		 BS02 >1hwt:B (identical to 1hwt:F)
    gctaatagcgataatagcgc
    		 ? GO:0000981 ... P0CS82 9886294
    867 1hwt:C
    (2.5)    		 BS03 >1hwt:E (identical to 1hwt:A)
    gcgctattatcgctattagc
    		 ? GO:0000981 ... P0CS82 9886294
    868 1hwt:C
    (2.5)    		 BS04 >1hwt:F (identical to 1hwt:B)
    gctaatagcgataatagcgc
    		 ? GO:0000981 ... P0CS82 9886294
    869 1hwt:D
    (2.5)    		 BS01 >1hwt:A (identical to 1hwt:E)
    gcgctattatcgctattagc
    		 ? GO:0000981 ... P0CS82 9886294
    870 1hwt:D
    (2.5)    		 BS02 >1hwt:B (identical to 1hwt:F)
    gctaatagcgataatagcgc
    		 ? GO:0000981 ... P0CS82 9886294
    871 1hwt:G
    (2.5)    		 BS01 >1hwt:A (identical to 1hwt:E)
    gcgctattatcgctattagc
    		 ? GO:0000981 ... P0CS82 9886294
    872 1hwt:G
    (2.5)    		 BS02 >1hwt:E (identical to 1hwt:A)
    gcgctattatcgctattagc
    		 ? GO:0000981 ... P0CS82 9886294
    873 1hwt:G
    (2.5)    		 BS03 >1hwt:F (identical to 1hwt:B)
    gctaatagcgataatagcgc
    		 ? GO:0000981 ... P0CS82 9886294
    874 1hwt:H
    (2.5)    		 BS01 >1hwt:A (identical to 1hwt:E)
    gcgctattatcgctattagc
    		 ? GO:0000981 ... P0CS82 9886294
    875 1hwt:H
    (2.5)    		 BS02 >1hwt:E (identical to 1hwt:A)
    gcgctattatcgctattagc
    		 ? GO:0000981 ... P0CS82 9886294
    876 1hwt:H
    (2.5)    		 BS03 >1hwt:F (identical to 1hwt:B)
    gctaatagcgataatagcgc
    		 ? GO:0000981 ... P0CS82 9886294
    877 1hys:A
    (3.0)    		 BS02 >1hys:F
    cttttcttttaaaaagtggctg
    		 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0003676 ... P03366 11250910
    878 1i3j:A
    (2.2)    		 BS01 >1i3j:B
    ttcttgggtctaccgtttaat
    		 3.1.-.- GO:0003677 ... P13299 11447104
    879 1i3j:A
    (2.2)    		 BS02 >1i3j:C
    aattaaacggtagacccaaga
    		 3.1.-.- GO:0003677 ... P13299 11447104
    880 1i6h:A
    (3.3)    		 BS01 >1i6h:D
    aaatgcctggtct
    		 2.7.7.6 GO:0000428 ... P04050 11313499
    881 1i6h:B
    (3.3)    		 BS01 >1i6h:D
    aaatgcctggtct
    		 2.7.7.6 GO:0000428 ... P08518 11313499
    882 1i6j:A
    (2.0)    		 BS01 >1i6j:B
    gtcgtc
    		 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.26.4
    3.4.23.-    		 N/A P03355 11526315
    883 1i6j:A
    (2.0)    		 BS02 >1i6j:C
    acgggacgac
    		 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.26.4
    3.4.23.-    		 N/A P03355 11526315
    884 1i7d:A
    (2.05)    		 BS01 >1i7d:B (identical to 2o19:D, 2o54:D, 2o59:D)
    cgcaactt
    		 5.6.2.1 GO:0000287 ... P14294 11429611
    885 1i8m:A
    (2.1)    		 BS01 >1i8m:D (identical to 1ehl:A, 6j7y:C, 5k97:G, 6kcp:E, 3px7:B, 7q8a:E, 1rh0:D, 1rh0:F, 3u7h:X, 6wg6:M, 6wg6:N, 1xhz:F)
    tt
    		 ? N/A Q7TS98 11733999 PDBbind: Kd=2700nM
    886 1i8m:B
    (2.1)    		 BS01 >1i8m:T (identical to 4a75:B, 4a75:F, 4a76:H, 5gkp:C, 5gkp:D, 4hqb:N, 5ip3:D, 2nmv:D, 2pjr:C, 2pjr:D, 6s3h:E, 6s3i:C, 8s9i:B, 3udg:D, 3udg:E, 3udg:G, 2vtb:G, 2vtb:H, 2vtb:I, 2vtb:J, 1xhz:E, 1xhz:G, 1xhz:H, 5zkl:B)
    ttttt
    		 ? N/A Q924Q6 11733999 PDBbind: Kd=2700nM
    887 1i8m:B
    (2.1)    		 BS02 >1i8m:D (identical to 1ehl:A, 6j7y:C, 5k97:G, 6kcp:E, 3px7:B, 7q8a:E, 1rh0:D, 1rh0:F, 3u7h:X, 6wg6:M, 6wg6:N, 1xhz:F)
    tt
    		 ? N/A Q924Q6 11733999 PDBbind: Kd=2700nM
    888 1i8m:H
    (2.1)    		 BS01 >1i8m:T (identical to 4a75:B, 4a75:F, 4a76:H, 5gkp:C, 5gkp:D, 4hqb:N, 5ip3:D, 2nmv:D, 2pjr:C, 2pjr:D, 6s3h:E, 6s3i:C, 8s9i:B, 3udg:D, 3udg:E, 3udg:G, 2vtb:G, 2vtb:H, 2vtb:I, 2vtb:J, 1xhz:E, 1xhz:G, 1xhz:H, 5zkl:B)
    ttttt
    		 ? N/A Q924Q6 11733999 PDBbind: Kd=2700nM
    889 1i8m:L
    (2.1)    		 BS01 >1i8m:T (identical to 4a75:B, 4a75:F, 4a76:H, 5gkp:C, 5gkp:D, 4hqb:N, 5ip3:D, 2nmv:D, 2pjr:C, 2pjr:D, 6s3h:E, 6s3i:C, 8s9i:B, 3udg:D, 3udg:E, 3udg:G, 2vtb:G, 2vtb:H, 2vtb:I, 2vtb:J, 1xhz:E, 1xhz:G, 1xhz:H, 5zkl:B)
    ttttt
    		 ? N/A Q7TS98 11733999 PDBbind: Kd=2700nM
    890 1iaw:A
    (2.4)    		 BS01 >1iaw:C
    gccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    891 1iaw:A
    (2.4)    		 BS02 >1iaw:D (identical to 1iaw:E, 1iaw:F)
    tgccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    892 1iaw:A
    (2.4)    		 BS03 >1iaw:E (identical to 1iaw:D, 1iaw:F)
    tgccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    893 1iaw:A
    (2.4)    		 BS04 >1iaw:F (identical to 1iaw:D, 1iaw:E)
    tgccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    894 1iaw:B
    (2.4)    		 BS01 >1iaw:C
    gccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    895 1iaw:B
    (2.4)    		 BS02 >1iaw:D (identical to 1iaw:E, 1iaw:F)
    tgccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    896 1iaw:B
    (2.4)    		 BS03 >1iaw:E (identical to 1iaw:D, 1iaw:F)
    tgccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    897 1iaw:B
    (2.4)    		 BS04 >1iaw:F (identical to 1iaw:D, 1iaw:E)
    tgccacgccggcgtggc
    		 3.1.21.4 GO:0003677 ... P50187 11473254
    898 1ic8:A
    (2.6)    		 BS01 >1ic8:E
    cttggttaataattcaccaga
    		 ? GO:0001889 ... P20823 12453420
    899 1ic8:A
    (2.6)    		 BS02 >1ic8:F
    tctggtgaattattaaccaag
    		 ? GO:0001889 ... P20823 12453420
    900 1ic8:B
    (2.6)    		 BS01 >1ic8:E
    cttggttaataattcaccaga
    		 ? GO:0001889 ... P20823 12453420
    Reference:
  • Chengxin Zhang, Xi Zhang, Peter L Freddolino, and Yang Zhang. BioLiP2: an updated structure database for biologically relevent ligand-protein interactions, Nucleic Acids Research, gkad630 (2023).
  • Jianyi Yang, Ambrish Roy, and Yang Zhang. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions, Nucleic Acids Research, 41: D1096-D1103 (2013) (download the PDF file).

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