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Primary Citation PubMed: 11080628 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 19

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Designing a nanotube using naturally occurring protein building blocks.

(2006) PLoS Comput Biol 2

PubMed: 16683021 | PubMedCentral: PMC1447657 | DOI: 10.1371/journal.pcbi.0020042

In the CA protein nanotube construction, the initial structure of the CA protein was taken from the crystal structure [ 25 ] available in the Protein Data Bank [ 26 ] (... DB code 1e6j, chain P).

Publication Year: 2006


Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

(2007) Nucleic Acids Res 35

PubMed: 17151070 | PubMedCentral: PMC1761437 | DOI: 10.1093/nar/gkl975

Peptides selected using the 17b, 13b5, Herceptin and Bo2C11 antibodies were mapped to the structure of their corresponding antigens, specified by the PDB identifiers 1G9M, 1E6J, 1N8Z and 1IQD, respect... vely ( Table 1 ).

Publication Year: 2007


Mutation in the loop C-terminal to the cyclophilin A binding site of HIV-1 capsid protein disrupts proper virus assembly and infectivity.

(2007) Retrovirology 4

PubMed: 17371591 | PubMedCentral: PMC1832212 | DOI: 10.1186/1742-4690-4-19

The figure was produced with PyMOL [27] and the structure was obtained from the Protein Data Bank (cf PDB entry 1E6J [3]).

Publication Year: 2007


Structural deformation upon protein-protein interaction: a structural alphabet approach.

(2008) BMC Struct Biol 8

PubMed: 18307769 | PubMedCentral: PMC2315654 | DOI: 10.1186/1472-6807-8-12

We consider the 3 classes from Table 3 , namely enzyme/substrate, antibody/antigen, and other; Table 3 Description of the complex set Type (number) Complexes PDB id Enzyme-substrate (23) 1ACB , 1AVX ,... 1AY7 , 1BVN , 1CGI , 1D6R , 1DFJ , 1E6E , 1EAW , 1EWY , 1EZU , 1F34 , 1HIA , 1KKL , 1MAH , 1PPE , 1TMQ , 1UDI , 2MTA , 2PCC , 2SIC , 2SNI , 7CEI Antibody-Antigen (10) 1AHW , 1BGX , 1BVK , 1DQJ , 1E6J , 1JPS , 1MLC , 1VFB , 1WEJ , 2VIS Other (35) 1A2K , 1AK4 , 1AKJ , 1ATN , 1B6C , 1BUH , 1DE4 , 1E96 , 1EER , 1F51 , 1FC2 , 1FQ1 , 1FQJ , 1GCQ , 1GP2 , 1GRN , 1H1V , 1HE1 , 1HE8 , 1I2M , 1I4D , 1IB1 , 1IBR , 1IJK , 1KLU , 1KTZ , 1KXP , 1M10 , 1ML0 , 1N2C , 1QA9 , 1RLB , 1SBB , 1WQ1 , 2BTF • the motif should be located in totality at the protein-protein interfaces of the complexes; • we do not consider runs of helical letters (A,a,V,W,Z,B,C) or extended letters (L,M,N,T,X,J,K).

Publication Year: 2008


Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

(2008) PLoS Comput Biol 4

PubMed: 18989394 | PubMedCentral: PMC2566816 | DOI: 10.1371/journal.pcbi.1000214

Thus, the following structures were used: Gag derived proteins: matrix p17, capsid p24, nucleocapsid p7 (PDB IDs: 1tam, 1e6j, 1a1t, respectively); Pol derived proteins: protease p10, reverse transcrip... ase p51, RNase p15, integrase p31 (PDB IDs: 1aaq, 1rtd, 1o1w, 2itg, respectively); Vpr p12/p10 (PDB ID: 1m8l); Tat p16/p14 (PDB ID: 1mnb); Rev p19 (PDB ID: 1etf); Vpu p16 (PDB ID: 1vpu); Env derived proteins: gp120, gp41 (PDB IDs: 1gc1, 1env, respectively); Nef p27/p25 (PDB ID: 2nef).

Publication Year: 2008


Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis.

(2008) BMC Bioinformatics 9

PubMed: 19087303 | PubMedCentral: PMC2639436 | DOI: 10.1186/1471-2105-9-538

In test cases three to eight, the six sets of mimotopes were obtained by screening phage display libraries with the 17b [ 22 ], 13b5 [ 22 ], Herceptin [ 40 ], Bo2C11 [ 41 ], Cetuximab Fab [ 42 ] and 8... D6A3 IgG [ 43 ] antibodies respectively (see Table 1 ), and their corresponding Ab-Ag complex structures have been resolved (PDB id: 1g9m , 1e6j , 1n8z , 1iqd , 1yy9 and 2adf ).

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqd 1yy9 2adf 1avz 1hx1 Average CED ID CE0179 CE0175 CE0058 CE0170 CE0096 CE0176 CE0199 CE0154 -- -- Epitope size 21 19 15 11 20 16 15 15 16 24 Antigen size 94 93 304 209 580 155 612 188 102 111 Pep-3D-Search TP/PE 19/40 7/13* 10/39 11/36 20/35* 6/47 10/25 12/36 10/39 13/39 MCC 0.3902 0.1442 0.1394 0.2285 0.1856 0.0356 0.1030 0.2153 0.1643 0.152 0.1758 Sensitivity 0.475 0.5833 0.2564 0.3056 0.5714 0.1277 0.4 0.3333 0.2564 0.3333 0.3642 Precision 0.9048 0.3684 0.6667 1.0 1.0 0.375 0.6667 0.8 0.625 0.5417 0.6948 PepSurf TP/PE 19/28 2/17 9/31 10/30 6/11 8/31 1/8* 10/18 14/25 12/25 MCC 0.4134 -0.0537 0.1257 0.2056 0.0596 0.1272 0.0067 0.1832 0.3348 0.1863 0.1589 Sensitivity 0.6786 0.1176 0.2903 0.3333 0.5455 0.2581 0.125 0.5556 0.56 0.48 0.3944 Precision 0.9048 0.1053 0.6 0.9091 0.3 0.5 0.0476 0.6667 0.875 0.5 0.5409 Mapitope TP/PE 19/22 2/18 13/33 1/6 9/13 15/106 3/23* 0/10 6/9* 5/21 MCC 0.4224 -0.062 0.1899 0.0154 0.0909 0.2401 0.0209 -0.0173 0.1387 0.0135 0.1053 Sensitivity 0.8636 0.1111 0.3939 0.1667 0.6923 0.1415 0.1304 0.0 0.6667 0.2381 0.3404 Precision 0.9048 0.1053 0.8667 0.0909 0.45 0.9375 0.1429 0.0 0.375 0.2083 0.4081 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqd 1yy9 2adf 1avz 1hx1 Average CA (distance threshold = 6.5) TP/PE 5/5 2/10 13/42 10/43 18/36* 7/31 2/10* 0/20 12/31 13/31 MCC 0.1119 -0.0014 0.1887 0.2033 0.1664 0.1015 0.019 -0.0367 0.262 0.1889 0.1204 Sensitivity 1.0 0.2 0.3095 0.2326 0.5 0.2258 0.2 0.0 0.3871 0.4194 0.3474 Precision 0.2381 0.1053 0.8667 0.9091 0.9 0.4375 0.1333 0.0 0.75 0.5417 0.4882 CA (distance threshold = 7) TP/PE 19/40 7/13* 10/39 11/36 20/35* 6/47 10/25 12/36 10/39 13/39 MCC 0.3902 0.1442 0.1394 0.2285 0.1856 0.0356 0.1030 0.2153 0.1643 0.152 0.1758 Sensitivity 0.475 0.5833 0.2564 0.3056 0.5714 0.1277 0.4 0.3333 0.2564 0.3333 0.3642 Precision 0.9048 0.3684 0.6667 1.0 1.0 0.375 0.6667 0.8 0.625 0.5417 0.6948 CA (distance threshold = 7.5) TP/PE 19/38 12/27* 10/45 9/33 18/40 0/36 7/25 12/36 9/37 9/36 MCC 0.3947 0.2349 0.1374 0.1812 0.1662 -0.0895 0.0704 0.2153 0.1332 0.0411 0.1485 Sensitivity 0.5 0.4444 0.2222 0.2727 0.45 0.0 0.28 0.3333 0.2432 0.25 0.2996 Precision 0.9048 0.6316 0.6667 0.8182 0.9 0.0 0.4667 0.8 0.5625 0.375 0.6126 CA (distance threshold = 8) TP/PE 20/39 12/28* 10/40 10/35 17/36 0/37 5/26 13/35 8/39 5/32 MCC 0.4248 0.2309 0.1391 0.2047 0.1565 -0.1144 0.0484 0.2378 0.0822 -0.065 0.1345 Sensitivity 0.5128 0.4286 0.25 0.2857 0.4722 0.0 0.1923 0.3714 0.2051 0.1563 0.2874 Precision 0.9524 0.6316 0.6667 0.9091 0.85 0.0 0.3333 0.8667 0.5 0.2083 0.5918 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

Furthermore, for the test cases 1jrh , 1g9m , 1e6j and 2adf , Pep-3D-Search and PepSurf gave better predictions, while Mapitope failed in the test cases 1e6j and 2adf .

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqd 1yy9 2adf 1avz 1hx1 Average CB (distance threshold = 6.5) TP/PE 5/5 0/0 11/43 11/38 15/30* 10/43 6/28 8/29 8/27 2/27 MCC 0.1119 0.0 0.155 0.2285 0.1379 0.1604 0.059 0.1316 0.1380 -0.1271 0.0995 Sensitivity 1.0 0.0 0.2558 0.2895 0.5 0.2326 0.2143 0.2759 0.2963 0.0741 0.3139 Precision 0.2381 0.0 0.7333 1.0 0.75 0.625 0.4 0.5333 0.5 0.0833 0.4863 CB (distance threshold = 7) TP/PE 13/18 6/9* 14/46 8/28 14/31* 9/46 9/29* 14/31 9/41 11/38 MCC 0.2747 0.1283 0.2048 0.1593 0.1282 0.127 0.0917 0.2604 0.1139 0.0939 0.1582 Sensitivity 0.7222 0.6667 0.3043 0.2857 0.4516 0.1957 0.3103 0.4516 0.2195 0.2895 0.3897 Precision 0.619 0.3158 0.9333 0.7273 0.7 0.5625 0.6 0.9333 0.5625 0.4583 0.6412 CB (distance threshold = 7.5) TP/PE 19/41 12/27 10/40 9/35 14/33** 2/45 8/28* 10/45 8/29 9/29 MCC 0.3879 0.2349 0.1391 0.1806 0.1279 -0.0837 0.0809 0.1626 0.13 0.084 0.1444 Sensitivity 0.4634 0.4444 0.25 0.2571 0.4242 0.0444 0.2857 0.2222 0.2759 0.3103 0.2978 Precision 0.9048 0.6316 0.6667 0.8182 0.7 0.125 0.5333 0.6667 0.5 0.375 0.5921 CB (distance threshold = 8) TP/PE 19/38 15/30 10/37 4/34* 18/37 4/42 7/26 10/18* 6/27 11/32 MCC 0.3947 0.3222 0.1401 0.0571 0.1664 -0.0101 0.0703 0.1832 0.0665 0.1271 0.1518 Sensitivity 0.5 0.5 0.2703 0.1176 0.4865 0.0952 0.2692 0.5556 0.2222 0.3438 0.3361 Precision 0.9048 0.7895 0.6667 0.3636 0.9 0.25 0.4667 0.6667 0.375 0.4583 0.5841 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

Here, we describe one experiment of the test case 1e6j (Table 6 ) in detail.

PDB ID Antibody Antigen References Library size * Antibody-antigen test cases 1jrh mAb A6 IFNgammaR Lang S et al.(2000) 59 × 5 1bj1 rhuMAb VEGF vascular endothelial growth factor ChenY et al. (1999) 36 × 6, 3 × 5, 2 × 4 1g9m mAb 17b gp120 Enshell-Seijffers D et al. (2003) 10 × 14,1 × 12 1e6j mAb 13b5 p24 Enshell-Seijffers D et al. (2003) 14 × 14, 2 × 7 1n8z Herceptin Fab Her-2 Riemer AB et al. (2004) 5 × 12 1iqd mAb Bo2C11 Coagulation factor VIII Villard S et al. (2003) 27 × 12 1yy9 Cetuximab Fab Epidermal Growth Factor Receptor Riemer AB et al. (2005) 4 × 10 2adf 82D6A3 IgG Von Willebrand factor Vanhoorelbeke K et al. (2003) 2 × 15, 3 × 6 Protein-protein test cases 1avz Fyn SH3 domain Nef Rickles RJ et al. (1994) 8 × 10, 10 × 12 1hx1 Bovine Hsc70 Bag chaperone regulator Takenaka IM et al. (1995) 8 × 15 *Number of sequences × sequence length.

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqds 1yy9 2adf 1avz 1hx1 Average AHA (distance threshold = 3.7) TP/PE 17/20 7/16 12/44 11/34 17/36* 6/32 6/25* 9/33 13/36 8/32 MCC 0.375 0.1243 0.1716 0.2286 0.1565 0.0733 0.0595 0.1502 0.2855 0.0351 0.1659 Sensitivity 0.85 0.4375 0.2727 0.3235 0.4722 0.1875 0.24 0.2727 0.3611 0.25 0.3667 Precision 0.8095 0.3684 0.8 1.0 0.85 0.375 0.4 0.6 0.8125 0.3333 0.6349 AHA (distance threshold = 4) TP/PE 16/20 7/10 13/42 8/30 15/30* 5/39 6/23 10/37 12/35 10/34 MCC 0.3491 0.1528 0.1887 0.1584 0.1379 0.0283 0.0598 0.1695 0.2525 0.0858 0.1583 Sensitivity 0.8 0.7 0.3095 0.2667 0.5 0.1282 0.2609 0.2703 0.3429 0.2941 0.3873 Precision 0.7619 0.3684 0.8667 0.7273 0.75 0.3125 0.4 0.6667 0.75 0.4167 0.6021 AHA (distance threshold = 4.3) TP/PE 16/18 8/11 14/42 8/36 17/30* 9/37 4/16* 11/37 10/33 4/26 MCC 0.3537 0.1773 0.2052 0.1558 0.1571 0.1431 0.0394 0.1923 0.1869 -0.0514 0.1559 Sensitivity 0.8889 0.7273 0.3333 0.2222 0.5667 0.2432 0.25 0.2973 0.303 0.1538 0.3986 Precision 0.7619 0.4211 0.9333 0.7273 0.85 0.5625 0.2667 0.7333 0.625 0.1667 0.6048 AHA (distance threshold = 4.6) TP/PE 19/36 9/24 9/44 4/41 18/38 0/34 8/25* 8/36* 5/37 6/27 MCC 0.3989 0.1483 0.1206 0.0495 0.1663 -0.1023 0.0813 0.1241 -0.0357 0.0051 0.0956 Sensitivity 0.5278 0.375 0.2045 0.0976 0.4737 0.0 0.32 0.2222 0.1351 0.2222 0.2578 Precision 0.9048 0.4737 0.6 0.3636 0.9 0.0 0.5333 0.5333 0.3125 0.25 0.4871 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

The test case 1e6j is taken from Mapitope and Mimox.

The structure of p24 with 13B5 has been resolved [PDB: 1e6j ], and the 13B5 epitope, which is composed of ALGPAATEE (204–210, 212, 213) TA (216–217), has been recorded in the CED database as CE0170.

Publication Year: 2008


Prediction of antigenic epitopes on protein surfaces by consensus scoring.

(2009) BMC Bioinformatics 10

PubMed: 19772615 | PubMedCentral: PMC2761409 | DOI: 10.1186/1471-2105-10-302

Methods Protein datasets Protein Dataset 1 48 antigen-antibody complexes with resolution <3.0 Å were selected from the 59 representative antigen-antibody complexes compiled by Ponomare... ko and Bourne[ 25 ]: 2ADF , 1FE8 , 1BGX , 1E6J , 1EGJ , 1FSK , 1H0D , 1IQD , 1JRH , 1LK3 , 1MHP , 1NL0 , 1NSN , 1OAZ , 1ORS , 1PKQ , 1RJL , 1SY6 , 1TZI , 1WEJ , 1YJD , 1YY9 , 1ZTX , 2JEL , 1A14 , 1NCA , 1BVK , 1JHL , 1NDG , 1P2C , 1JPS , 1AR1 , 1EO8 , 1QFU , 1EZV , 1OSP , 1FJ1 , 1FNS , 1G9M , 1R3J , 1N8Z , 1NFD , 1TQB , 2VDL , 1V7M , 1XIW , 2AEP , and 1R0A .

Publication Year: 2009


Protein-protein docking using region-based 3D Zernike descriptors.

(2009) BMC Bioinformatics 10

PubMed: 20003235 | PubMedCentral: PMC2800122 | DOI: 10.1186/1471-2105-10-407

HEX ZDOCK LZerD Complex Rank lRMSD HITS2K Rank lRMSD HITS2K Rank lRMSD HITS2K 1ACB 694 8.3 3 185 9.98 5 21 9.98 2 1AHW 234 8 3 34 9.86 20 5 2.68 43 1AKJ 209 9.6 10 - - - - - - 1AVX 108 8.9 7 604 9.43 ... - - - 1AY7 645 9.9 4 568 9.39 11 1884 6.13 1 1B6C 593 9 2 182 5.6 10 73 6.2 10 1BUH 743 7.7 2 - - - 599 9.73 1 1BVK - - - 70 7.56 1125 9.83 10 1BVN 63 9.1 20 29 8.65 52 2 6.89 49 1CGI 42 9.4 17 145 3.88 32 86 8.13 12 1D6R 447 7.7 1 303 8.44 3 344 7.84 8 1DE4 946 8.6 1 - - - - - - 1DFJ 17 9.5 14 5 6.64 67 - - - 1DQJ - - - 152 9.82 23 - - - 1E6E 109 5.6 10 - - - 52 4.49 10 1E6J - - - 12 5.34 93 87 9.97 20 1E96 - - - - - - 1375 8.91 1 1EAW 9 5 20 3 5.43 87 6 9.95 19 1EER 609 9.2 8 - - - - - - 1EWY 76 9.1 12 22 8.08 51 103 9.91 110 1EZU - - - - - - 815 7.89 3 1F34 124 6.7 11 5 5.45 20 - - - 1F51 371 9.6 5 602 9.78 4 1101 8.31 1 1FQJ 41 8 12 - - - 1014 9.63 3 1FSK 5 1.8 16 1 4.04 149 15 6.23 28 1GHQ - - - - - - 1571 9.14 1 1GRN 914 9.1 2 1704 5.81 2 1407 7.41 2 1HE1 37 6.4 18 23 8.14 8 47 6.2 7 1HIA 51 8.7 6 - - - 1 9.49 74 1I4D - - - - - - 286 9.11 2 1I9R 82 2.1 8 104 9.07 16 104 9.41 10 1IJK 1012 8.7 3 - - - - - - 1IQD - - - 492 8.99 11 41 6.46 27 1JPS - - - 171 8.51 7 292 2.01 20 1K4C 21 9.6 1 - - - 219 9.78 6 1KAC 687 8.7 1 - - - 655 3.95 3 1KXP 36 9.4 13 1616 7.11 2 1226 8.05 1 1KXQ 488 7.1 5 116 7.58 29 73 4.33 16 1M10 514 9.5 2 - - - - - - 1MAH 2 1.2 20 92 3.86 9 92 2.43 2 1ML0 - - - 36 2.87 35 121 5.71 2 1MLC 408 3.6 2 110 6.17 12 1834 4.48 1 1NCA 116 1.2 5 14 7.08 49 270 9.97 2 1NSN 142 1.5 6 185 5.07 19 94 8.61 4 1PPE 2 9.7 47 1 0.86 358 1 2.26 184 1QA9 - - - - - - 546 8.07 6 1QFW - - - 257 8.63 4 108 9.54 2 1TMQ 356 5.9 9 314 6.12 11 50 3.71 11 1UDI 8 6.2 9 32 8.04 34 19 6.4 16 1VFB - - - 22 8.52 65 150 8.7 22 1WEJ - - - 81 8.36 42 156 9.82 18 1WQ1 125 7.1 10 610 9.9 5 32 9.79 11 2BTF - - - 553 6.39 3 - - - 2JEL 164 6 3 45 4.49 86 66 6.81 35 2MTA 136 9 4 - - - 4 7.57 48 2QFW - - - - - - 68 9.01 11 2SIC 57 8.8 8 173 8.62 18 127 4.59 6 2SNI 256 9.6 7 534 9.69 4 - - - 7CEI 61 8.7 5 106 7.11 28 - - - Summary HEX ZDOCK LZerD Mean 206 173 164 Rank<100 17 19 22 Rank<500 32 33 34 Rank<1000 42 39 38 Rank<2000 43 41 47 Win 18 20 22 The results of HEX are taken from the columns of "U-U shape-only Blind search" in Table 3 of the paper by Ritchie et al .

Original ZDOCK Rank Context Shapes (CS) PatchDock ZDOCK Decoys Reranked by LZerD Score LZerD Complex Rank a) iRMSD HIT2K Rank iRMSD RMSD iRMSD Rank iRMSD HIT2K Rank iRMSD HIT2K 1AHW 268 2.28 21 402 2.46 181 2.49 15 1.68 50 5 1.34 42 1AK4 - b) - - - - - - (NA NA NA) 43787 2.35 0 1AKJ 4872 2.29 0 - - - - 1985 1.93 1 - - - 1AVX 2863 2.23 0 - - - - 5689 2.22 0 786 2.41 2 1AY7 5584 1.33 0 - - - - 394 1.1 7 1884 1.98 1 1B6C 1717 2.43 2 - - - - 497 2.13 8 1001 2.41 1 1BJ1 129 0.86 49 1893 1.93 - - 306 1.01 20 298 1.86 7 1BUH 14556 2.37 0 - - - - 11230 2.42 0 12251 1.6 0 1BVK 3970 1.94 0 - - 2754 2.27 9560 2.43 0 5515 2.24 0 1BVN 502 1.97 13 34 2.34 - - 8 2.26 59 27 2.32 6 1CGI 145 2.44 9 - - 1120 2.11 1775 2.14 1 9041 2.1 0 1D6R 2951 2.03 0 - - - - 5022 2.49 0 2619 2.24 0 1DFJ 9 2.27 40 - - - - 9350 2.14 0 - - - 1DQJ 2287 2.48 0 - - - - 5391 2.32 0 20816 2.09 0 1E6E 22643 2.08 0 - - - - 432 1.94 2 52 2.13 8 1E6J 15 1.56 34 - - - - 2509 1.81 0 439 2.18 8 1E96 3094 2.26 0 - - - - 882 1.88 2 216 2.14 2 1EAW 3 1.54 62 94 2.29 85 2.29 5 1.48 111 20 2.42 10 1EWY 259 2.32 2 - - - - 1007 2.14 4 349 2.36 14 1EZU 1100 1.94 3 - - - - 589 1.42 4 824 1.21 2 1F34 5 2.2 13 - - 490 1.81 5082 1.61 0 - - - 1F51 230 2.18 4 - - - - 154 1.76 5 3545 1.58 0 1FQJ 9889 2.29 0 - - - - 628 2.39 2 - - - 1FSK 1 1.63 105 20 1.57 221 2.39 29 1.57 76 15 2.4 11 1GCQ 24339 2.29 0 - - - - 39221 2.29 0 9418 1.8 0 1GHQ - - - - - - - (NA NA NA) 15357 1.68 0 1GRN 1704 2.34 2 - - - - 1884 1.74 1 1407 2.18 1 1HE1 4672 1.31 0 1029 2.17 - - 51 2 8 267 1.98 2 1HIA - - - - - - - (NA NA NA) 44189 2.42 0 1I9R 50 2.45 41 - - - - 57 1.96 10 95 2.39 21 1IJK 52731 2.44 0 - - - - 39460 2.44 0 6731 2.45 0 1IQD 612 2.27 5 - - - - 36 0.99 27 41 1.2 18 1JPS 171 1.81 9 - - - - 5305 1.37 0 292 0.9 20 1K4C 20806 1.53 0 - - - - 4468 1.18 0 1188 1.43 7 1KAC 2896 2.33 0 - - - - 1313 2.33 1 655 2.18 3 1KTZ 53599 1.69 0 - - - - 33926 1.69 0 12162 1.19 0 1KXP 1734 2.36 1 - - - - 32023 1.91 0 14208 2.22 0 1KXQ 212 1.91 13 2226 1.73 - - 629 1.24 4 73 1.68 14 1MAH 92 1.31 9 597 1.16 887 2.28 541 0.89 6 92 0.87 2 1ML0 36 1.56 21 - - 231 2.02 406 1.37 6 559 2.38 3 1MLC 110 1.19 12 18 2.28 - - 243 1.07 12 1834 1.16 1 1NCA 14 1.93 47 - - - - 302 1.55 12 12528 1.5 0 1NSN 185 1.81 5 26 1.79 - - 147 1.81 13 945 2.29 1 1PPE 1 0.57 218 2 2.31 - - 1 0.72 194 1 0.83 68 1QA9 5672 1.88 0 - - - - 5924 1.82 0 1381 2.19 3 1QFW 257 1.14 7 597 1.73 - - 136 2.31 17 108 1.24 4 1RLB - - - - - - - (NA NA NA) 46073 1.24 0 1TMQ 314 1.88 11 783 1.68 1 1.96 90 1.45 19 50 1.45 5 1UDI 258 2.17 4 2649 2.14 27 2.42 219 2.39 3 59 2.36 6 1VFB 2734 1.79 0 228 2.46 - - 1534 1.61 1 1303 1.69 1 1WEJ 465 2.37 8 - - - - 916 1.97 1 3914 2.06 6 1WQ1 1101 2.49 2 - - - - 284 2.05 2 141 1.87 2 2JEL 45 1.79 33 - - - - 149 2.44 19 133 2.49 9 2MTA - - - - - 515 2.19 (NA NA NA) 606 1.64 11 2PCC - - - - - - - (NA NA NA) 4542 2.31 0 2QFW 832 2.29 3 33 2.32 - - 42 1.99 17 68 1.55 29 2SIC 173 1.86 24 1077 2.28 - - 17 1.85 61 12 2.04 9 2SNI 17906 2.44 0 - - - - 428 2.33 2 - - - 7CEI 106 1.97 24 2290 1.9 366 1.07 705 1.57 7 6765 2.03 0 Summary c) ZDOCK CS PatchDock (PD) LZerD Rerank LZerD Rank<100 11 7 3 11 14 Rank<500 26 9 6 26 23 Rank<1000 29 12 9 32 29 Rank<2000 33 15 10 38 36 Wins vs. LZerD Rerank ZDOCK/LZerD Rerank 26/26 CS/LZerD Rerank 5/34 PD/LZerD Rerank 7/34 - - Wins vs. LZerD ZDOCK/LZerD 24/33 CS/LZerD 5/34 PD/LZerD 8/34 LZerD Rerank/LZerD 24/28 - LZerD results are compared with ZDOCK, Context Shapes, and PatchDock.

Publication Year: 2009


Automated detection of conformational epitopes using phage display Peptide sequences.

(2009) Bioinform Biol Insights 3

PubMed: 20140073 | PubMedCentral: PMC2808184 | DOI: null

35 – 37 Mapping of mAb 13b5 epitopes A list of fourteen 12-mer cysteine-loop peptides of mAb 13b5 18 that bind HIV-1 capsid protein (p24) 38 , 39 (PDB id: 1E6J) were selected.

Publication Year: 2009


Sampling the conformation of protein surface residues for flexible protein docking.

(2010) BMC Bioinformatics 11

PubMed: 21092317 | PubMedCentral: PMC3002368 | DOI: 10.1186/1471-2105-11-575

Table 1 The different docking test cases included in our experiments Complex PDB ID 1ACB 1AHW 1AK4 1AKJ 1AY7 1B6C 1BJ1 1BKD 1BUH 1BVK 1BVN 1CGI 1D6R 1DFJ 1DQJ 1E6E 1E6J 1EAW 1EER 1EWY 1FC2 1FSK 1GHQ 1... 9R 1IBR 1IQD 1KAC 1KTZ 1KXQ 1M10 1MAH 1ML0 1MLC 1NCA 1NSN 1QFW 1R0R 1S1Q 1SBB 1TMQ 1UDI 1VFB 1WEJ 1WQ1 1Y64 2AJF 2B42 2FD6 2I25 2JEL 2MTA 2QFW a 2SIC 2UUY 2VIS 7CEI a Note that the name 2QFW does not correspond to the actual PDB file with this ID.

Publication Year: 2010


MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries.

(2011) BMC Bioinformatics 12

PubMed: 21609501 | PubMedCentral: PMC3124435 | DOI: 10.1186/1471-2105-12-199

In general, MimoPro performed better in 1ZTX, 2ADF and 2GHW but slightly worse in 1G9M and 1E6J than both PepSurf and Pep-3D-Search did.

PepSurf was the best performer in cases 1G9M, 1E6J, 3IU3 and 2NY7 but the worst in 1N8Z, 2ADF and 1ZTX, and even failed in 1N8Z*.

Publication Year: 2011


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ(N 5 ) [σ(N 5 )] P success Irmsd CAPRI quality PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd CAPRI quality 1OPH rigid-body | E... 5 5.0 [0.0] 1.00 0.23 *** 1YVB rigid-body | E 4 4.0 [0.9] 0.71 1.32 ** 1ML0 rigid-body | O 5 5.0 [0.0] 1.00 0.40 *** 1ZHI rigid-body | O 4 4.0 [0.9] 0.72 1.47 ** 1KTZ rigid-body | O 5 5.0 [0.0] 1.00 0.51 *** 1XQS medium | O 4 3.9 [1.0] 0.70 1.47 ** 1PPE rigid-body | E 5 5.0 [0.0] 1.00 0.91 *** 2OOB rigid-body | O 4 3.9 [1.2] 0.69 1.04 ** 1B6C rigid-body | O 5 5.0 [0.0] 1.00 1.51 ** 1DFJ rigid-body | E 4 3.6 [1.4] 0.57 1.39 ** 2HLE rigid-body | O 5 5.0 [0.2] 1.00 0.89 *** 1BJ1 rigid-body | AB 4 3.6 [1.2] 0.57 2.25 * 1KXP rigid-body | O 5 5.0 [0.2] 1.00 1.16 ** 2CFH medium | O 4 3.6 [1.1] 0.56 1.25 ** 2HRK medium | O 5 5.0 [0.2] 0.99 1.42 ** 1BVK rigid-body | A 3 3.5 [1.2] 0.51 1.77 ** 1QA9 rigid-body | O 5 5.0 [0.1] 1.00 0.59 *** 1AVX rigid-body | E 3 3.4 [1.1] 0.50 1.87 ** 1FSK rigid-body | AB 5 5.0 [0.1] 1.00 1.03 ** 1MAH rigid-body | E 3 3.4 [1.1] 0.50 1.94 ** 1JPS rigid-body | A 5 4.9 [0.5] 0.97 1.15 ** 1VFB rigid-body | A 4 3.4 [1.1] 0.50 1.96 ** 1AK4 rigid-body | O 5 4.9 [0.5] 0.97 1.36 ** 2SNI rigid-body | E 3 3.3 [1.1] 0.47 1.14 ** 1UDI rigid-body | E 5 4.9 [0.4] 0.98 2.17 * 1KXQ rigid-body | AB 3 3.3 [1.1] 0.44 1.25 ** 1D6R rigid-body | E 5 4.9 [0.3] 0.99 2.14 * 1BUH rigid-body | O 3 3.3 [1.1] 0.44 1.73 ** 7CEI rigid-body | E 5 4.8 [0.6] 0.94 0.79 *** 1XD3 rigid-body | O 3 3.3 [1.1] 0.45 2.69 * 2UUY rigid-body | E 5 4.7 [0.7] 0.93 1.30 ** 1E4K difficult | A 4 3.2 [1.3] 0.45 1.98 ** 1E6E rigid-body | E 5 4.7 [0.6] 0.94 0.79 *** 1E6J rigid-body | A 3 3.2 [1.2] 0.40 2.48 * 1SBB rigid-body | O 5 4.6 [0.7] 0.91 0.60 *** 1HIA rigid-body | E 3 3.2 [1.1] 0.40 1.95 ** 2C0L difficult | O 5 4.6 [0.7] 0.91 1.15 ** 2SIC rigid-body | E 3 3.1 [1.3] 0.40 0.59 *** 1IQD rigid-body | AB 5 4.5 [0.8] 0.89 1.26 ** 2FD6 rigid-body | A 3 3.1 [1.2] 0.38 1.85 ** 1AHW rigid-body | A 5 4.5 [0.7] 0.89 1.38 ** 1HE1 rigid-body | O 3 3.0 [1.2] 0.36 1.31 ** 1GCQ rigid-body | O 5 4.4 [0.8] 0.88 0.72 *** 2JEL rigid-body | AB 3 3.0 [1.1] 0.36 0.40 *** 1EAW rigid-body | E 4 4.4 [0.8] 0.87 1.31 ** 1AY7 rigid-body | E 3 2.9 [1.1] 0.32 1.55 ** 1FC2 rigid-body | O 4 4.4 [0.8] 0.84 1.53 ** 1WQ1 medium | O 3 2.8 [1.3] 0.30 1.48 ** 1GPW rigid-body | O 4 4.4 [0.8] 0.88 1.98 ** 2QFW rigid-body | AB 3 2.8 [1.2] 0.30 0.64 *** 2MTA rigid-body | E 4 4.3 [0.9] 0.81 0.66 *** 1IJK medium | E 3 2.8 [1.2] 0.28 2.35 * 1BVN rigid-body | E 4 4.0 [1.0] 0.72 1.35 ** 1NCA rigid-body | AB 3 2.7 [1.3] 0.27 0.46 *** 1CGI rigid-body | E 4 4.0 [1.0] 0.74 1.76 ** 2I25 rigid-body | A 3 2.2 [1.2] 0.15 1.80 ** 10.1371/journal.pone.0022477.

Publication Year: 2011


Consensus structural models for the amino terminal domain of the retrovirus restriction gene Fv1 and the murine leukaemia virus capsid proteins.

(2004) BMC Struct Biol 4

PubMed: 14715087 | PubMedCentral: PMC331416 | DOI: 10.1186/1472-6807-4-1

(a) EIAV (b) RSV SEED 1eia 12084543 pdb-1E6J 0–210 6358699 gb-AAF07324 131–342 8072301 gb-AAF71968 0–155 6815746 gb-AAF28696 0–173 6649692 gb-AAF21520 5–224 120... 4543 pdb-1E6J 3–210 120850 sp-P18041 97–362 27803398 gb-AAO21890 120–281 294961 gb-AAA74706 116–381 5106563 gb-AAD39752 81–346 SEED 1d1dA (c) HIV-1 (d) HTLV-I 6358699 gb-AAF07324 129–340 SEED 1qrjA 22037894 gb-AAM90230 148–359 12084543 pdb-1E6J 0–210 SEED 1e6jP 22037894 gb-AAM90230 144–370 532325 gb-AAA99545 50–224 9886907 gb-AAG01643 0–222 9886907 gb-AAG01643 0–211 MLV Modelling The databank search using the MLV sequence as a probe provided a useful collection of six sequences (Table 1(a) ) which, with the MLV probe sequence itself, were passed through the PsiPred secondary structure prediction protocol (Methods Sect n .)

Publication Year: 2004


Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.

(2012) BMC Struct Biol 12

PubMed: 22554255 | PubMedCentral: PMC3427047 | DOI: 10.1186/1472-6807-12-6

Further, of the 3 cases showing large length variation between the bound and unbound forms (PDB codes: 1gcq, 1qa9, 1e6j) only 1e6j features in our analysis of cases showing structural changes away fro... the interface.

Publication Year: 2012


Structure of a novel shoulder-to-shoulder p24 dimer in complex with the broad-spectrum antibody A10F9 and its implication in capsid assembly.

(2013) PLoS One 8

PubMed: 23620741 | PubMedCentral: PMC3631186 | DOI: 10.1371/journal.pone.0061314

The structures of the BMJ4 p24 dimer in complex with the A10F9 Fab fragment were determined by molecular replacement using Fab 13B5 as the search model (PDBID: 1E6J).

The structure of the complex was determined by molecular replacement using the Fab 13B5 fragment (PDBID: 1E6J) as the search model, and the crystallographic statistics are listed in Table 1 .

(B) Ribbon representation of an overall view of p24 CTD recognition by Fab13B5 (PDBID: 1E6J).

We performed a structural comparison of our Fab fragment structure with the crystal structure of the Fab13B5 fragment recognizing the C-terminal domain of an intact p24 mutant at 3 Å resolution (PDBID: 1E6J) [20] .

Publication Year: 2013


DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.

(2014) PLoS One 9

PubMed: 24586799 | PubMedCentral: PMC3931789 | DOI: 10.1371/journal.pone.0089466

For five protein-protein complexes, no near-native solution could be found at all by DrugScore PPI /FRODOCK: Three of them are antigen-antibody complexes (see above; PDB-IDs: 1E6J, 1I9R, 2HMI), and tw... are other complexes (PDB-IDs: 1GLA, 1I4D).

Publication Year: 2014


Inhibitors of peptidyl proline isomerases as antivirals in hepatitis C and other viruses.

(2014) PLoS Pathog 10

PubMed: 25375953 | PubMedCentral: PMC4223064 | DOI: 10.1371/journal.ppat.1004428

NMR solution structures (left, 1GWP) and multiple crystallographic models of CA (center, 1MG3, 1E6J, 3P05) highlight the structural variability of the Pro loop that is minimized by Cyclophilin A bindi... g (right, 1AK4, 1M9C, 1M9D).

Publication Year: 2014


IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.

(2014) BMC Bioinformatics 15 Suppl 16

PubMed: 25521441 | PubMedCentral: PMC4290663 | DOI: 10.1186/1471-2105-15-S16-S9

As a result, some first hits found by F 2 Dock obtained low ranks, e.g. for the case of [PDB:1E6J] (Antigen/Antibody - type easy), the first hit was ranked at rank 126 by F 2 Dock, but ranked at rank ... by the IFACEwat.

Publication Year: 2014


Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2.

(2015) J Struct Funct Genomics 16

PubMed: 25575462 | PubMedCentral: PMC4329188 | DOI: 10.1007/s10969-014-9192-z

An initial phase for the AdipoR2Δ99·Fv43 complex was obtained by molecular replacement using the Fv fragment (the V H and V L fragments from PDB IDs 1E6J and 1FDL, respectively) in Pha... er [ 37 ] as search models.

Publication Year: 2015