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PDB ID Mentions in PubMed Central Article count: 16

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PDB ID Mentions in PubMed Central

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Antibody-protein interactions: benchmark datasets and prediction tools evaluation.

(2007) BMC Struct Biol 7

PubMed: 17910770 | PubMedCentral: PMC2174481 | DOI: 10.1186/1472-6807-7-64

The authors of a few structures clearly stated in their papers that antibody-protein contacts in the complexes were different: [PDB: 1MLC, 1NFD, 1OB1, 1P2C, 1QFW].

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


Common physical basis of macromolecule-binding sites in proteins.

(2008) Nucleic Acids Res 36

PubMed: 18988628 | PubMedCentral: PMC2602788 | DOI: 10.1093/nar/gkn868

Liang and co-workers ( 67 ) showed that residues at the interfaces of eight ‘nonobligate’ heterodimeric protein ‘complexes’ (PDB entries 1ppf, 1cho, 1fss, 1brs, 2sic, 2... tc, 2sni and 1mlc) have higher sidechain energies than the other surface residues.

Publication Year: 2008


A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.

(2007) Proteins 69

PubMed: 17623864 | PubMedCentral: PMC2673351 | DOI: 10.1002/prot.21498

Table I The Number of Top 5 Decoys with rmsd < 10 Å given by EMPIRE and the RosettaDock scoring function Pdb ID a 1CGI 1CHO 2PTC 1TGS 2SNI 2SIC 1CSE 2KAI EMPIRE b 1 5 4 5 5 5 5 5 Roset... aDock c 4 3 2 5 4 5 2 4 Pdb ID 1BRC 1ACB 1BRS 1MAH 1UGH 1DFJ 1FSS 1AVW EMPIRE 5 3 4 5 5 5 3 5 RosettaDock 1 2 4 5 5 4 5 5 Pdb ID 1PPE 1TAB 1UDI 1STF 2TEC 4 HTC 1MLC 1WEJ EMPIRE 5 5 5 5 5 5 2 2 RosettaDock 5 5 5 5 5 5 0 0 Pdb ID 1AHW 1DQJ 1BVK 1FBI 2JEL 1BQL 1JHL 1NQA EMPIRE 0 1 1 5 5 2 1 5 RosettaDock 5 2 5 3 5 5 1 5 Pdb ID 1NMB 1MEL 2VIR 1EO8 1QFU 1IAI 2PCC 1WQ1 EMPIRE 5 5 3 1 4 3 4 4 RosettaDock 5 5 4 1 5 0 3 3 Pdb ID AVZ 1MDA 1IGC 1ATN 1GLA 1SPB 2BTF 1A0Q EMPIRE 0 4 1 5 5 5 3 4 RosettaDock 0 3 2 5 1 5 4 1 Pdb ID 1BTH 1FIN 1FQ1 1GOT 1EFU 3HHR #(≥3) d #(>) EMPIRE 0 0 4 5 2 2 39 21 e RosettaDock 0 0 2 0 0 0 34 10 f a Enzyme/Inhibitor: the first 22 protein complexes (1CGI-4HTC); antibody-antigen: the next 16 protein complexes (1MLC-1IAI); the others: (2PCC to 1A0Q); and the difficult set (1BTH to 3HHR).

Publication Year: 2007


Single domain antibodies: promising experimental and therapeutic tools in infection and immunity.

(2009) Med Microbiol Immunol 198

PubMed: 19529959 | PubMedCentral: PMC2714450 | DOI: 10.1007/s00430-009-0116-7

d Chicken lysozyme in complex with the VL and VH domains of a conventional mouse mAb (pdb code 1mlc).

Publication Year: 2009


SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models.

(2010) PLoS Comput Biol 6

PubMed: 20098500 | PubMedCentral: PMC2800046 | DOI: 10.1371/journal.pcbi.1000644

Global docking is considerably more computationally demanding, and thus we restricted our tests of global docking to five targets, and to simulate a practical docking application, chose only those tar... ets for which unbound crystal structures were available for both the antibody and the antigen: 1MLC, 1AHW, 1JPS, 1WEJ and 1VFB.

Unbound Crystal Structures RosettaAntibody Homology Model Standard RosettaDock Standard RosettaDock EnsembleDock SnugDock EnsembleDock-plus-SnugDock Co-Crystal PDB ID Top Decoy Top 10 Decoys Top Decoy Top 10 Decoys Top Decoy Top 10 Decoys Top Decoy Top 10 Decoys Top Decoy Top 10 Decoys 1mlc 0 ** 0 0 0 0 0 0 0 * 1ahw ** ** 0 0 * * * * ** ** 1jps ** *** 0 * 0 * 0 * ** ** 1wej 0 * 0 0 0 0 * * 0 ** 1vfb 0 * 0 0 0 0 0 0 0 0 Refer to Table 1 key for explanation.

Publication Year: 2010


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.

PDB a) Class b) Difficulty c) #Atoms (R, L) d) ΔASA (Å 2 ) e) 3DZD Correlation for Bound interface 3DZD Correlation for Unbound interface 1AY7 ( 1RGH ; 1A19 ) E E 747,721 1237 0.93 0.93 1CGI ( 2CGA ; 1HPT ) E E 1800,441 2053 0.96 0.97 2PCC ( 1CCP ; 1YCC ) E E 2339,847 1141 0.99 0.98 2SNI ( 1UBN ; 2CI2 ) E E 1932,521 1628 0.97 0.95 1ACB ( 2CGA ; 1EGL ) E MD 1799,575 1544 0.94 0.95 1AHW ( 1FGN ; 1TFH ) A E 3304,1622 1899 0.99 0.98 1FSK ( 1FSK ; 1BV1 ) A E 3347,1231 1623 0.95 0.89 1MLC ( 1MLB ; 3LZT ) A E 3290,1000 1392 0.97 0.96 1NCA ( 1NCA ; 7NN9 ) A E 3329,3067 1953 0.99 0.99 2JEL ( 2JEL ; 1POH ) A E 3297,640 1501 0.92 0.90 1KXP ( 1IJJ ; 1KW2 ) O E 2782,3527 3341 0.96 0.97 1IB1 ( 1QJB ; 1KUY ) O MD 3673,1312 2808 0.95 0.87 1WQ1 ( 6Q21 ; 1WER ) O MD 2534,1351 2913 0.92 0.93 1ATN ( 1IJJ ; 3DNI ) O D 2942,2036 1774 0.95 0.97 1DE4 ( 1A6Z ; 1CX8 ) O D 3064,1351 2066 0.98 0.97 a) The PDB IDs for the unbound proteins are shown in brackets.

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


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 Classification PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification 1K74 rigid-body ... O 2 2.5 [1.1] 0.20 1.63 RB sampling 1EER difficult | O 1 0.9 [1.0] 0.02 2.23 BB sampling 1Z5Y rigid-body | O 2 2.4 [1.1] 0.16 1.14 BB sampling 1FAK difficult | O 1 0.9 [0.9] 0.01 3.30 discrimination 1WEJ rigid-body | A 2 2.2 [1.1] 0.14 2.60 discrimination 1TMQ rigid-body | E 1 0.8 [0.9] 0.01 1.47 RB sampling 1HE8 medium | O 2 2.2 [1.1] 0.13 3.19 BB sampling 1I4D rigid-body | O 1 0.8 [0.9] 0.01 3.13 RB sampling 1ATN difficult | O 2 2.1 [1.2] 0.12 1.53 RB sampling 1RLB rigid-body | O 1 0.8 [0.9] 0.01 3.88 RB sampling 2HQS rigid-body | O 2 2.1 [1.2] 0.13 2.69 BB sampling 1Z0K rigid-body | O 1 0.7 [0.8] 0.00 3.56 BB sampling 1JMO difficult | O 2 2.1 [1.2] 0.11 2.82 BB sampling 1EFN rigid-body | O 1 0.7 [0.8] 0.00 3.58 BB sampling 2O8V rigid-body | E 2 2.1 [1.2] 0.12 3.62 BB sampling 1I9R rigid-body | AB 1 0.6 [0.8] 0.00 0.52 RB sampling 1J2J rigid-body | O 2 2.0 [1.4] 0.14 1.10 BB sampling 1AZS rigid-body | O 0 0.5 [0.9] 0.01 5.41 RB sampling 1NSN rigid-body | AB 2 2.0 [1.2] 0.10 1.15 discrimination 2B42 rigid-body | E 0 0.4 [0.6] 0.00 5.85 RB sampling 1K5D medium | O 2 2.0 [1.1] 0.09 2.87 BB sampling 2BTF rigid-body | O 0 0.3 [0.6] 0.00 4.44 BB sampling 1FQ1 difficult | E 2 1.7 [1.3] 0.08 2.18 RB sampling 1KKL medium | E 0 0.2 [0.5] 0.00 4.60 RB sampling 2AJF rigid-body | O 2 1.7 [1.1] 0.06 1.23 RB sampling 1F51 rigid-body | O 0 0.2 [0.5] 0.00 12.35 BB sampling 1E96 rigid-body | O 1 1.6 [1.1] 0.05 3.38 BB sampling 1KAC rigid-body | O 0 0.1 [0.5] 0.00 4.01 BB sampling 1I2M medium | O 1 1.5 [1.0] 0.03 2.68 BB sampling 1MLC rigid-body | A 0 0.1 [0.4] 0.00 4.31 BB sampling 1QFW rigid-body | AB 1 1.5 [1.1] 0.03 1.93 RB sampling 1S1Q rigid-body | O 0 0.1 [0.3] 0.00 4.37 BB sampling 1GLA rigid-body | O 2 1.5 [1.1] 0.05 2.98 BB sampling 1M10 medium | E 0 0.0 [0.0] 0.00 4.46 BB sampling 1AKJ rigid-body | O 1 1.2 [1.0] 0.02 1.48 BB sampling 1A2K rigid-body | O 0 0.0 [0.0] 0.00 5.20 BB sampling 1EZU rigid-body | E 1 1.2 [1.0] 0.02 2.82 RB sampling 1R8S difficult | O 0 0.0 [0.0] 0.00 5.21 BB sampling 1F34 rigid-body | E 1 1.2 [1.0] 0.02 4.00 RB sampling 1GP2 medium | O 0 0.0 [0.0] 0.00 5.23 BB sampling 1GRN medium | O 1 1.1 [1.0] 0.02 1.24 BB sampling 1IBR difficult | O 0 0.0 [0.0] 0.00 5.46 RB sampling 1NW9 medium | E 1 1.1 [1.0] 0.02 2.33 BB sampling 1BKD difficult | O 0 0.0 [0.0] 0.00 5.62 BB sampling 2H7V medium | O 1 1.1 [1.0] 0.02 3.65 BB sampling 2OT3 difficult | O 0 0.0 [0.0] 0.00 6.00 BB sampling 1GHQ rigid-body | O 1 1.0 [1.0] 0.01 2.69 BB sampling 1FQJ rigid-body | O 0 0.0 [0.0] 0.00 6.48 RB sampling 2NZ8 medium | O 1 1.0 [1.0] 0.02 3.91 BB sampling 1PXV difficult | E 0 0.0 [0.0] 0.00 9.49 BB sampling 1IB1 medium | O 1 1.0 [1.0] 0.01 3.95 discrimination 1H1V difficult | O 0 0.0 [0.0] 0.00 9.96 BB sampling 1K4C rigid-body | AB 1 1.0 [1.1] 0.02 2.15 BB sampling 1Y64 difficult | O 0 0.0 [0.0] 0.00 13.70 discrimination 1EWY rigid-body | E 1 1.0 [1.1] 0.02 3.01 BB sampling 1DQJ rigid-body | A 0 0.0 [0.2] 0.00 6.15 BB sampling 2PCC rigid-body | E 1 1.0 [0.9] 0.01 3.38 discrimination 1ACB medium | E 0 0.0 [0.1] 0.00 4.56 RB sampling 1KLU rigid-body | O 0 0.0 [0.1] 0.00 8.16 BB sampling Unsuccessful docking predictions are classified as cases for which the five lowest-energy decoys did not contain at least three near-native structures.

Publication Year: 2011


Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.

(2012) PLoS Comput Biol 8

PubMed: 22253587 | PubMedCentral: PMC3257286 | DOI: 10.1371/journal.pcbi.1002351

For instance, the complex between Fab 44.1 and HEW lysozyme (1MLC) undergoes only minor conformational change (IRMSD 0.60 Å), yet has a small rate of association (around [31] ).

Publication Year: 2012


Protein docking prediction using predicted protein-protein interface.

(2012) BMC Bioinformatics 13

PubMed: 22233443 | PubMedCentral: PMC3287255 | DOI: 10.1186/1471-2105-13-7

The second example (Figure 9B ) is monoclonal antibody fab d44.1 complexed with lysozyme (1MLC).

Publication Year: 2012


Predicting protein interactions by Brownian dynamics simulations.

(2012) J Biomed Biotechnol 2012

PubMed: 22500075 | PubMedCentral: PMC3303761 | DOI: 10.1155/2012/121034

Complex PDB Res (Å) Receptorname Ligandname Docking results Crystal structures RMSD a (Å) Interaction energy (kcal mol −1 ) RMSD (Å) Interaction energy (kcal mol "... 2;1 ) Sequence number/total number b Protease-inhibitor  1CA0 2.10 Chymotrypsin APPI 1.27 −93.70 0.84 −93.22 116522/492124  1CBW 2.60 Chymotrypsin BPTI 0.54 −83.51 0.19 −85.02 171485/456398  1ACB 2.00 Chymotrypsin Eglin C 1.00 −103.41 0.70 −103.49 382613/513612  1CHO 1.80 Chymotrypsin Ovonmuciod 0.30 −102.35 0.38 −102.42 302176/406978  1CGI 2.30 Chymotrypsinogen HPTI 0.18 −147.17 0.15 −147.10 34660/494274  2KAI 2.50 Kallikrein A BPTI 1.10 −114.68 0.21 −113.85 422991/576133  2SNI 2.10 Subtilisin BPN CI-2 0.27 −108.81 0.28 −108.86 232574/428140  2SIC 1.80 Subtilisin BPN SSI 0.89 −94.41 0.20 −104.20 109196/440000  1CSE 1.20 Subtilisin Carlsberg Eglin C 1.24 −98.28 0.088 −103.19 284340/470409  2TEC 1.98 Thermitase Eglin C 0.44 −108.55 0.68 −109.99 341844/565586  1TAW 1.80 Trypsin (bovine) APPI 1.10 −97.13 0.86 −97.14 374416/448887  2PTC 1.90 Trypsin (bovine) BPTI 0.98 −96.22 0.36 −96.25 269684/377757  3TGI 1.80 Trypsin (rat) BPTI 0.39 −102.43 0.52 −102.44 232589/511269  1BRC 2.50 Trypsin (rat) APPI 1.43 −90.55 0.55 −90.04 120053/527160 Enzyme-inhibitor  1FSS 3.00 Acetylcholinesterase Fasciculin II 0.17 −137.88 0.20 −137.88 356416/364018  1BVN 2.50 α -Amylase Tendamistat 0.25 −142.67 0.24 −142.51 202279/297696  1BGS 2.60 Barnase Barstar 0.48 −112.46 0.57 −112.37 326865/408756  1AY7 1.70 Ribonuclease sa Barstar 0.49 −77.41 0.51 −77.37 9999/356359  2B5R 1.70 TEM-1 lactamase BLIP 0.78 −154.04 0.37 −158.39 369/464219  1UGH 1.90 UDG UGI 0.54 −135.58 0.51 −135.43 120973/427026 Electron transport  2PCB c 2.80 Cyt c Peroxidase Cytochrome c 1.98 −87.18 0.22 −81.79 6060/416861  2PCF NMR Cytochrome f Plastocyanin 0.28 −118.96 0.23 −119.32 83197/208700 Antibody-antigen  1MLC 2.10 Fab D44.1 Lysozyme 1.59 −93.99 0.44 −95.80 75843/344243  1VFB d 1.80 Fv D1.3 Lysozyme 0.53 −84.78 0.43 −84.59 517225/1195007 a RMSDs are calculated for the C α atoms of the ligand protein since the receptor proteins are always fixed during the simulations.

Complex PDB RMSD (Å) a Other docking methods ICM b Nussinov c FTDOCK d BiGER e Protease-inhibitor  1CA0 0.44 0.4 — — —  1CBW 0.24 0.5 — —  1ACB 0.58 0.5 0.9 — 0.6  1CHO 0.26 0.3 0.5 0.8 —  1CGI 0.15 0.4 — 1.0 —  2KAI 0.30 0.8 1.2 0.4  2SNI 0.16 0.3 1.1 0.6 —  2SIC 0.58 0.4 1.1 0.8 3.8  1CSE 0.53 0.3 1.3 — —  2TEC 0.18 0.3 1.2 — 3.6  1TAW 0.39 0.7 — — —  2PTC 0.72 0.4 0.6 0.7  3TGI 0.21 0.3 — — —  1BRC 0.55 0.7 — — — Enzyme-inhibitor  1FSS 0.13 0.4 — — —  1BVN 0.23 0.4 — — —  1BGS 0.33 0.6 — —  1AY7 0.30 0.7 — —  2B5R 0.60 1.3 — — —  1UGH 0.39 0.4 — — — Electron transport  2PCB 1.18 1.2 — — —  2PCF 0.19 1.1 — — — Antibody-antigen  1MLC 0.57 0.4 — 0.8 —  1VFB 0.24 0.5 1.5 0.7 — a RMSDs are calculated for the ligand interface C α atoms in this work.

Publication Year: 2012


Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

(2013) PLoS Comput Biol 9

PubMed: 23696727 | PubMedCentral: PMC3656110 | DOI: 10.1371/journal.pcbi.1003072

Protein structures for the D1.3-lysozyme and D44.1-lysozyme complexes were retrieved from PDB-structures 1VFB [63] and 1MLC [88] , respectively, and crystal waters at the protein-protein interface wer... included in the starting structures of the associated states.

Publication Year: 2013


The structural basis of antibody-antigen recognition.

(2013) Front Immunol 4

PubMed: 24115948 | PubMedCentral: PMC3792396 | DOI: 10.3389/fimmu.2013.00302

PDB IDs 1JHL, 3D9A, and 1MLC were superimposed according to HEL structure.

Publication Year: 2013


The malaria parasite egress protease SUB1 is a calcium-dependent redox switch subtilisin.

(2014) Nat Commun 5

PubMed: 24785947 | PubMedCentral: PMC4024747 | DOI: 10.1038/ncomms4726

Molecular replacement calculations using PDB ID: 1MLC (mouse monoclonal IgG1 Fab D44.1) and 1BH6 ( Bacillus licheniformis , subtilisin Carslberg) as the search models for the Fab fragments and rPfSUB1... at, respectively, were carried out in the programme AutoMR, identifying a clear solution with a log-likelihood gain of 1747 and good packing.

Publication Year: 2014


OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.

(2014) PLoS One 9

PubMed: 25153121 | PubMedCentral: PMC4143332 | DOI: 10.1371/journal.pone.0105954

Peptide Protein PDB RMSD PDB RMSD PDB RMSD PDB RMSD 1ACY 1.79 2G5B 1.86 1BJ1 2.11 3DVG 2.71 1CE1 2.35 2H1P 2.98 1DZB 1.35 3E8U 2.40 1CFS 2.41 2HFG 2.50 1EGJ 3.74 3ETB 2.35 1CFT 1.93 2HH0 2.30 1FBI 2.7... 3G6D 3.23 1CU4 1.99 2HKF 2.17 1I9R 2.48 3IU3 2.67 1E4W 2.35 2HRP 1.69 1JHL 1.55 3KS0 2.31 1EJO 1.47 2IGF 2.48 1JRH 4.68 3L5W 1.80 1F90 1.69 2J4W 1.83 1KIQ 1.86 3L5Y 1.96 1FPT 1.61 2OQJ 2.62 1MLC 3.42 3LQA 3.88 1GGI 2.43 2OR9 1.79 1NSN 2.12 3NFP 3.09 1HH6 2.02 2OSL 2.85 1OAZ 2.28 3NH7 2.96 1HIN 1.86 2QHR 2.77 1ORS 3.23 3O0R 4.05 1I8I 1.89 2QSC 2.79 1RJL 1.84 3P30 3.79 1JP5 1.86 2R0W 2.02 1TQB 2.23 3QWO 1.97 1KC5 2.06 2ZPK 2.19 1TZH 3.89 3RKD 3.24 1KCR 3.08 3BAE 1.75 1TZI 3.88 1KTR 2.13 3BKY 2.61 1V7M 2.82 1MVU 1.28 3CVH 3.13 1W72 2.69 1N64 1.55 3CXD 2.56 1XIW 2.10 1NAK 2.57 3EYU 2.42 1ZTX 1.96 1OBE 4.05 3F58 2.50 2BDN 1.77 1P4B 2.70 3FFD 2.78 2DQJ 2.03 1PZ5 2.31 3FN0 2.64 2FJH 3.75 1QKZ 2.03 3G5V 1.75 2HVK 1.44 1QNZ 2.27 3GGW 2.24 2IFF 3.52 1SM3 2.36 3GHB 1.92 2JEL 2.74 1TET 2.56 3GHE 1.56 2QR0 4.28 1TZG 1.69 3GJG 2.91 2R29 2.28 1U8J 2.17 3HR5 2.27 2VWE 4.30 1UWX 1.74 3MLR 2.16 2VXQ 1.88 1XGY 2.05 3MLS 1.88 2VXS 3.52 2A6I 2.33 3MLW 2.37 2ZUQ 2.49 2B1H 2.14 3MLX 2.08 3AB0 2.36 2CK0 2.82 3MLY 2.48 3BDY 2.94 2EH8 2.35 3QG6 2.48 3D85 2.63 Average Std Min Max Medium Accepted Failure Peptide 2.25 0.47 1.28 4.05 30% 69% 1% Protein 2.75 0.84 1.35 4.68 20% 72% 8% Four representative positioning successes of PDB 1MVU, 1NQZ, 1DZB and 2FEL with RMSDs of 1.28, 2.27, 1.35 and 2.74 Å, respectively, are illustrated in Figure 3 .

Publication Year: 2014