1PPE

THE REFINED 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND CMTI-I, A TRYPSIN INHIBITOR FROM SQUASH SEEDS (CUCURBITA MAXIMA): TOPOLOGICAL SIMILARITY OF THE SQUASH SEED INHIBITORS WITH THE CARBOXYPEPTIDASE A INHIBITOR FROM POTATOES


Citations in PubMed

Primary Citation PubMed: 2914611 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 11

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

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


Computational study for protein-protein docking using global optimization and empirical potentials.

(2008) Int J Mol Sci 9

PubMed: 19325720 | PubMedCentral: PMC2635596 | DOI: null

of acceptable 1A0O 4.10 0 4.16 0 3.08 1 1ACB 1.33 D 6 0.97 9 1.28 8 1AVZ 5.73 0 4.79 0 4.90 0 1BRC 5.29 0 4.04 0 5.03 0 1BRS 10.47 0 4.96 0 7.67 0 1CGI 3.46 3 2.73 5 2.94 1 1CHO 4.02 0 1.11 3 1.45 2 1... SE 3.29 2 1.27 2 1.62 3 1MEL 9.38 0 3.66 1 7.31 0 1PPE 4.07 0 3.11 6 2.40 8 1STF 4.98 0 4.95 0 4.96 0 1TAB 5.86 0 4.98 0 5.97 0 1TGS 1.64 1 5.87 0 5.24 0 1UDI 2.14 4 4.05 0 2.25 4 2KAI 5.66 0 5.28 0 5.55 0 2PTC 5.29 0 4.98 0 5.61 0 2TEC 2.63 4 2.60 1 2.37 3 4HTC 6.14 0 7.54 0 3.57 1 A complex pdb stands for the pdb ID of the native structure of the corresponding complex-complex structures B The RMSD is defined as the RMSD over C α atoms of the interface residues between a predicted structure and its native complex and the smallest RMSD is the RMSD value calculated for the most native-like conformation in the final set C The number of the acceptable native-like structures found in the final set of 500 conformations D The smallest RMSD being “acceptable” is written with bold italic types.

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


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

(2009) BMC Bioinformatics 10

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

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.... 6 181 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.

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 4 - - - 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 .

Publication Year: 2009


Designing coarse grained-and atom based-potentials for protein-protein docking.

(2010) BMC Struct Biol 10

PubMed: 21078143 | PubMedCentral: PMC2996388 | DOI: 10.1186/1472-6807-10-40

Table 5 Ranking ZDOCK2.3 decoys (IRMSD ≤2.5Å) by the jackknife test Complex Rank a ADPs-II b Zdock2.3 1B6C 311 168 1BVK - - 1DQJ - - 1EWY 754 113 1IJK 1131 - 1AVX 955 449 1D6R - - 1E96... 326 399 1F34 - 26 1GCQ - - 1GRN 492 807 1KXP 381 7 1NSN - 445 1SBB - - 1AKJ - 96 1AY7 236 - 1DFJ 720 1 1EAW 152 13 1I9R 329 90 1UDI 386 13 2PCC - - 1AHW 23 56 1BUH 16 - 1E6E 2 103 1ML0 10 1 1PPE 3 1 1QFW 1080 74 1TMQ 9 126 1WEJ 3 102 2JEL 307 86 7CEI 42 1 1BJ1 6 18 1CGI - - 1F51 1 11 1KAC - 1523 1NCA 4 4 1QA9 - - 2SNI 17 - 1RLB 48 302 Top10 8 (20.5%) 6 (15.4%) a-Rank of the lowest energy near-native decoy with IRMSD ≤2.5Å out of 54000 predictions.

Table 4 Ranking ZDOCK2.3 decoys (IRMSD ≤4Å) by the jackknife test Complex a Rank b ADPs-II c Zdock2.3 DARS ACE 1AK4 - - 950 1744 1B6C 95 16 9 178 1BVK 12 268 610 - 1DQJ - 1490 - - 1EWY 164 18 42 364 1FC2 484 - 24 797 1GHQ - - - 1308 1HIA 21 653 122 - 1IJK 1131 - 368 - 1KLU - - - - 1AVX 5 46 6 59 1D6R 1840 567 - - 1E96 39 399 42 490 1F34 13 26 666 5 1GCQ 1030 - 1057 1040 1GRN 210 102 - - 1I4D 84 403 965 616 1KXP 91 7 1 200 1NSN 53 445 - - 1SBB - - - - 1ACB 113 55 24 98 1AKJ 592 40 - - 1AY7 120 100 - - 1DFJ 37 1 - - 1EAW 65 13 33 309 1FQ1 - - - - 1GP2 4 389 58 1681 1I9R 184 14 589 - 1UDI 27 13 1 1 2PCC 203 193 821 120 1AHW 23 14 - - 1BUH 14 - 555 - 1E6E 2 103 44 520 1ML0 10 1 9 32 1PPE 3 1 1 1 1QFW 544 74 - - 1TMQ 9 126 12 22 1WEJ 3 42 1047 - 2JEL 307 86 76 579 7CEI 15 1 920 708 1ATN - - - - 1BJ1 6 18 18 85 1CGI 71 247 13 24 1F51 1 11 251 797 1KAC 121 1389 - - 1KKL 283 - 1 222 1NCA 4 4 - - 1QA9 687 - - - 2SNI 17 618 1 2 1RLB 48 302 5 7 a-Complex PDB code.

Publication Year: 2010


CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

(2011) PLoS One 6

PubMed: 21464987 | PubMedCentral: PMC3064578 | DOI: 10.1371/journal.pone.0017695

This final set of chains (109) consisted of all chains in the benchmark except 1FC2 chain C, 1ML0 chain A, 1PPE chain I and both chains of 1HE8, 2PCC and 1H1V.

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


Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

(2013) PLoS One 8

PubMed: 23874954 | PubMedCentral: PMC3712918 | DOI: 10.1371/journal.pone.0069365

Rigid-body (34) 1AK4 1AVX 1AY7 1B6C 1BUH 1BVN 1CGI 1D6R 1DFJ 1E6E 1E96 1EAW 1EWY 1F34 1FC2 1FQJ 1GCQ 1GHQ 1HE1 1KAC 1KTZ 1KXP 1KXQ 1MAH 1PPE 1QA9 1SBB 1TMQ 1UDI 2BTF 2PCC 2SIC 2SNI 7CEI Medium Difficu... ty (6) 1ACB 1GRN 1HE8 1I2M 1M10 1WQ1 Difficult (4) 1ATN 1FQ1 1H1V 1IBR Definition of IFP and Similarity between Decoys As suggested previously, it is sufficient to compare the interacting fragments rather than the whole structures to obtain information on near-native molecular interactions [9] , [10] .

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

In Figure 2 the DrugScore PPI scores for 1000 “unbound perturbation” decoys of a serine protease/prosegment complex (PDB-ID 1PPE) and a trypsin/trypsin inhibitor complex (PDB ID 1SPB) ... re shown as a function of the rmsd with respect to the native structure.

(A) Serine protease/prosegment complex (PDB-ID 1PPE); (B) trypsin/trypsin inhibitor complex (PDB ID 1SPB).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4443796

Rigid-body (21) 1AK4, 1AVX, 1AY7, 1B6C, 1CGI, 1D6R, 1E96, 1EAW, 1EWY, 1GCQ, 1GHQ, 1HE1, 1KAC, 1KTZ, 1PPE, 1SBB, 1UDI, 2PCC, 2SIC, 2SNI, 7CEI Medium Difficulty (2) 1ACB, 1GRN Table 3 The 44 complex str... ctures selected from the ZLAB Benchmark 2.0 dataset (small dataset).

Rigid-body (34) 1AK4, 1AVX, 1AY7, 1B6C, 1BUH, 1BVN, 1CGI, 1D6R, 1DFJ, 1E6E, 1E96, 1EAW, 1EWY, 1F34, 1FC2, 1FQJ, 1GCQ, 1GHQ, 1HE1, 1KAC, 1KTZ, 1KXP, 1KXQ, 1MAH, 1PPE, 1QA9, 1SBB, 1TMQ, 1UDI, 2BTF, 2PCC, 2SIC, 2SNI, 7CEI Medium Difficulty (6) 1ACB, 1GRN, 1HE8, 1I2M, 1M10, 1WQ1 Difficult (4) 1ATN, 1FQ1, 1H1V, 1IBR Table 4 The 120 complex structures selected from the ZLAB Benchmark 4.0 dataset (large dataset).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4459952

Protocol testing A subset of three complexes (pdb-entries: 1PPE, 2OUL and 2SIC) was chosen as an independent protocol test set.

PDB ID MC REMC WTE-REMC WTE-H-REMC 1PPE 5.6 Å 1.5 Å 2.2 Å 1.0 Å 14.5 h 14 h 12.3 h 17.8 h 2OUL 4.2 Å 1.9 Å 2.2 Å 0.7 Å 21.8 h 18.3 h 18 h 22 h 2SIC 4.9 Å 0.4 Å 2.8 Å 0.5 Å 25.5 h 22 h 19 h 20 h For all complexes, the best sampled L_rmsd and the execution time on 27 threads are listed.

Publication Year: 2015