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PDB ID Mentions in PubMed Central Article count: 18

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PDB ID Mentions in PubMed Central

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Spatial chemical conservation of hot spot interactions in protein-protein complexes.

(2007) BMC Biol 5

PubMed: 17925020 | PubMedCentral: PMC2231411 | DOI: 10.1186/1741-7007-5-43

Sens. 1a4y:A RNase inhibitor Angiogenin 4 0.74 0.78 0.75 0.18 0.78 0 0.75 0.8 14 1brs:A Barnase Barstar 6 0.75 1 0.5 n/a n/a n/a 0.5 0.67 8 1brs:D Barstar Barnase 6 1 1 1 n/a n/a n/a 1 1 6 1cbw I BPTI... Trypsin 7 1 0.88 1 0.75 0.62 1 0.75 1 9 1gc1:C CD4 gp120 6 0.74 0.86 0.67 0.58 0.62 0.67 0.81 0.33 49 1bxi:A Im9 E9 DNase 6 0.72 1 0.44 0.72 0.88 0.56 0.88 0.44 28 1dan:L Factor VII Tissue Factor 6 1 0.73 1 0.23 0.64 0 0.73 1 107 1jck:A TCR Vb SEC3 6 0.65 0.88 0.4 0.41 0.75 0 1 0.5 24 1jck:B SEC3 TCR Vb 6 0.75 1 0.5 0.31 0.5 0.12 1 0.62 10 1vfb:C HEL D.1.3 7 0.51 0.62 0.5 0.27 0.62 0.25 1 0 12 3hfm:Y HEL HYHEL 8 0.62 0.6 0.67 0.78 0.7 0.67 0.8 1 13 3hhr:A hGH hGHbp 4 0.74 1 0.52 0.59 0.44 0.68 0.94 0.32 161 Mean MAPPIS Mean Consurf Mean Robetta Total 6 0.77 0.86 0.66 0.48 0.66 0.4 0.85 0.64 440 (116) We compared the predictive power of MAPPIS with our previously developed multiple alignment methods.

Publication Year: 2007


PEPOP: computational design of immunogenic peptides.

(2008) BMC Bioinformatics 9

PubMed: 18234071 | PubMedCentral: PMC2262870 | DOI: 10.1186/1471-2105-9-71

In the last two Ab-Ag complexes [PDB: 1VFB , 1EY0 ], the predicted residues almost equally distribute into three clusters, thus yielding the lowest sensitivity numbers.

Publication Year: 2008


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


Identification of hot-spot residues in protein-protein interactions by computational docking.

(2008) BMC Bioinformatics 9

PubMed: 18939967 | PubMedCentral: PMC2579439 | DOI: 10.1186/1471-2105-9-447

Complex X-ray structures (PDB codes 1JCK and 1VFB , respectively).

Table 1 Initial dataset of complexes used in this work Complex a Res b Receptor Ligand Unbound receptor Res b Unbound ligand Res b Complex type c 1A22 2.60 Growth hormone receptor Growth hormone - - 1HGU 2.50 B/U 1A4Y 2.00 Ribonuclease inhibitor Angiogenin - - 1UN3 1.70 B/U 1AHW 3.00 Fab 5G9 Tissue Factor 1K6Q 2.40 2HFT 1.69 U/U 1AIE 1.50 p53 p53 - - - - B/B 1BRS 2.00 Barnase Barstar 1A2P 1.50 - - U/B 1BXI 2.05 Colicin E9 Immunity protein Im9 1FSJ 1.80 - - U/B 1DAN 2.00 Tissue Factor Factor VII 2HFT 1.69 - - U/B 1DFJ 2.30 Ribonuclease A Ribonuclease inhibitor 1FS3 1.40 2BNH 2.30 U/U 1DN2 2.70 IgG1 Fc fragment DCAWHLGELV WCT-NH 2 1H3V 3.10 - - U/B 3HFM 3.00 HYHEL-10 HEL 1GPO 1.95 3LZT 0.92 U/U 1GC1 2.50 CD4 gp120 1CDJ 2.50 - - U/B 1F47 1.95 Zipa FTSZ fragment 1F7W NMR - - U/B 1FC2 2.80 Fc fragment Protein A - - - - B/B 1FCC 3.50 Fc fragment Protein G 1H3V 3.10 - - U/B 1IAR 2.60 IL-4 receptor IL-4 - - 1HIK 2.60 B/U 1JCK 3.50 T-cell antigen receptor SEC3 1BEC 1.70 1CK1 2.60 U/U 1JRH 2.80 Antibody A6 Interferon-γ receptor - - - - B/B 1JTD 2.30 TEM-1 β-lactamase BLIP 1ZG4 1.55 - - U/B 1NMB 2.50 NC10 Neuraminidase N9 - - 7NN9 2.00 B/U 2PTC 1.90 Trypsin BPTI 1S0Q 1.02 1G6X 0.86 U/U 1VFB 1.80 Antibody D1.3 HEL - - 3LZT 0.92 B/U a PDB Code, b Resolution in Å; c B, Bound; U, Unbound For most of the complexes, the structure of only one of the two partners is available in the unbound conformation.

Complex Number of predicted residues( NIP ≥ 0.4) hot-spot prediction success(PPV) Number of near-native poses a 1BRS 5 100% 25 1BXI 6 67% 6 1DFJ 3 100% 8 1DN2 1 100% 5 1F47 3 67% 1 1JCK 7 100% 0 b 1JRH 2 50% 10 1NMB 1 100% 0 c 1VFB 9 67% 1 3HFM 3 100% 0 d 1IAR 7 71% 1 1AIE 4 50% 3 a Number of near-native solutions (RMSD ≤ 10 Å) within the ensemble of 100 lowest-energy docking orientations used to calculate the NIP values; b best RMSD within the ensemble is 22.0 Å; c best RMSD is 20.9 Å; d best RMSD is 12.2 Å.

Successful hot-spot predictions We report here two examples, corresponding to the SEC3 super antigen in complex with T-cell receptor β-chain (complex PDB 1JCK ), and D1.3 IgG1 in complex with HEL (complex PDB 1VFB ).

This dataset (Table 1 ) includes enzymes-ligand/inhibitor complexes (PDB code: 1JTD , 1BRS , 1BXI , 1A4Y , 1DFJ , 2DAN , 2PTC ), antibody-antigen complexes (PDB code: 1DN2 , 1FCC , 3HFM , 1FC2 , 1NMB , 1AHW , 1VFB , 1JRH , 1JCK ) and other types of interaction (PDB code: 1IAR , 1AIE , 1F47 , 1CG1 , 1A22 ).

Publication Year: 2008


Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces.

(2008) BMC Bioinformatics 9

PubMed: 18939984 | PubMedCentral: PMC2596146 | DOI: 10.1186/1471-2105-9-448

Protein A Protein B ΔG (kJ/mole) PDB Ref BPTI Chymotrypsin -44.96 1CBW [ 49 ] Barnase Barstar -79.50 1B27 [ 50 ] Subtilisin Carlsberg OMTKY3 -59.31 1R0R [ 51 ] Rap1A Raf1 -35.98 1C1Y [ 52 ] Ra... Byr2 -38.45 1K8R [ 53 ] Fv D1.3 Fv E5.2 -45.48 1DVF [ 54 ] Fv D1.3 HEWL -45.10 1VFB [ 55 ] BPTI Trypsin -75.16 2PTC [ 49 ] HyHEL10 Fab HEWL -56.21 3HFM [ 56 ] RalGDS Ras -35.15 1LFD [ 57 ] Subtilisin Carlsberg Eglin C -54.76 1CSE [ 58 ] IM9 Colicin E9 -78.62 1EMV [ 59 ] HyHEL5 Fab HEWL -59.36 1YQV [ 60 ] SGPB OMTKY3 -61.45 3SGB [ 61 ] Ribonuclease Inhibitor Angiogenin -87.15 1A4Y [ 62 ] N9 Neuraminidase NC10 Fab -48.50 1NMB [ 63 ] Subtilisin BPN' SSI -61.33 2SIC [ 64 ] Thrombin Thrombomodulin -53.09 1DX5 [ 65 ] Ribonuclease A Ribonuclease Inhibitor -76.30 1DFJ [ 62 ] Kallikrein A BPTI -51.83 2KAI [ 66 ] Protein constituents of the complexes are given, with the following abbreviations: OMTKY3, turkey ovomucoid third domain; HEWL, Hen Egg White Lysozyme; BPTI, Bovine Pancreatic Trypsin Inhibitor; IM9, Immunity Protein 9; SGPB Streptomyces griseus protease B; SSI, Streptomyces Subtilisin Inhibitor.

Publication Year: 2008


'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces.

(2009) Bioinformatics 25

PubMed: 19179356 | PubMedCentral: PMC2654803 | DOI: 10.1093/bioinformatics/btp058

However, only 13 of them are matched with PDB entries: 1a4y, 1ahw, 1brs, 1bxi, 1cbw, 1dan, 1dvf, 1gc1, 1jck, 1vfb, 2ptc, 2hfm and 3hhr.

Numbers of very warm and hot residues of the 13 protein complexes stored in ASEdb in comparison to those contained in our biclique patterns PDB ΔΔ G ≥1.5 kcal/mol ΔΔ G ≥2.0 kcal/mol ASEdb Biclique ASEdb Biclique 1A4Y 4 4 3 3 1AHW 1 1 1 1 1BRS 10 9 9 8 1BXI 7 7 6 6 1CBW 1 1 1 1 1DAN 6 6 3 3 1DVF 19 18 8 8 1GC1 1 0 0 0 1JCK 6 5 4 4 1VFB 6 5 3 3 2PTC 1 1 1 1 3HFM 6 5 5 4 3HHR 14 11 8 7 Total 82 73 52 49 sensitivity 73/82=89% 49/52=94% The larger ΔΔ G the residues are, more likely those are in our biclique patterns.

Publication Year: 2009


A feature-based approach to modeling protein-protein interaction hot spots.

(2009) Nucleic Acids Res 37

PubMed: 19273533 | PubMedCentral: PMC2677884 | DOI: 10.1093/nar/gkp132

The 17 protein–protein complexes analyzed PDB id First molecule Second molecule 1a4y RNase inhibitor Angiogenin 1a22 Human growth hormone Human growth hormone binding protein 1ahw Immunoglobul... n Fab5G9 Tissue factor 1brs Barnase Barstar 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 1cbw BPTI Trypsin inhibitor Chymotrypsin 1dan Blood coagulation factor VIIA Tissue factor 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 1f47 Cell division protein ZIPA Cell division protein FTSZ 1fc2 Fc fragment Fragment B of protein A 1fcc Fc (IGG1) Protein G 1gc1 Envelope protein GP120 CD4 1jrh Antibody A6 Interferon-gamma receptor 1nmb N9 Neuramidase Fab NC10 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 2ptc BPTI Trypsin 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 An independent test set An independent test set is constructed from the BID ( 35 ) to further validate our SVM model.

Structural comparison between the unbound and bound states for various proteins using combinatorial extension Bound state a Unbound state b RMSD(Å) c Seq. PDB id Chain id PDB id Chain id identity (%) Angiogenin 1a4y B 1un3 A 0.76 99.1 hGH 1a22 A 1hgu – d 2.68 68.4 Tissue factor e 1ahw C 1tfh A 1.39 100.0 Barnase 1brs A 1bnf A 1.12 98.1 Barstar 1brs D 1a19 A 0.44 98.9 BPTI 1cbw D 1bpt – d 0.39 98.2 Tissue factor e 1dan T 1tfh A 0.63 100.0 RNase inhibitor 1dfj I 2bnh – d 1.50 100.0 CD4 1gc1 C 1cdj A 1.09 100.0 Hen egg lysozyme e 1vfb C 1lyz – d 1.11 100.0 Trypsin 2ptc I 1bpt – d 0.36 98.2 Lysozyme e 3hfm Y 1lyz – d 0.67 100.0 a A protein is in the bound state.

Publication Year: 2009


Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods.

(2009) BMC Bioinformatics 10

PubMed: 19878545 | PubMedCentral: PMC2777894 | DOI: 10.1186/1471-2105-10-365

In the latter case, both structure are included in the data set (in practise this issue arises for only one pair of structures, PDB codes 3HFM and 1VFB ).

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

Notably, other cases with poor loop models dock successfully (e.g. 1VFB, 2B2X), but typically those cases have interfaces which do not involve as many CDR H3 contacts.

Thus one target (1VFB) which had succeeded in local docking failed in global docking due to low-scoring non-native decoys (see docking energy landscapes, Supporting Information Figure S2 ).

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 targets 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.

Publication Year: 2009


APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.

(2010) BMC Bioinformatics 11

PubMed: 20377884 | PubMedCentral: PMC2874803 | DOI: 10.1186/1471-2105-11-174

Table 1 Training set of protein structures PDB First molecule Second molecule 1a4y Angiogenin Ribonuclease Inhibitor 1a22 Human growth hormone Human growth hormone binding protein 1ahw Immunoglobulin ... ab 5G9 Tissue factor 1brs Barnase Barstar 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 1cbw BPTI Trypsin inhibitor Chymotrypsin 1dan Blood coagulation factor VIIA Tissue factor 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 1fc2 Fc fragment Fragment B of protein A 1fcc Fc (IGG1) Protein G 1gc1 Envelope protein GP120 CD4 1jrh Antibody A6 Interferon-gamma receptor 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 2ptc BPTI Trypsin 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 Independent test set An independent test set was extracted from the BID database [ 11 ] to further assess the performance of our proposed method.

Publication Year: 2010


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 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


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


Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces.

(2012) BMC Bioinformatics 13

PubMed: 22452998 | PubMedCentral: PMC3373366 | DOI: 10.1186/1471-2105-13-51

The interface between an anti-hen egg white lysozyme antibody D1.3 and a hen egg white lysozyme ([PDB: 1VFB ], resolution: 1.8 Å, wetness: 0.083, rWBL: 1.143).

Publication Year: 2012


A semi-supervised boosting SVM for predicting hot spots at protein-protein interfaces.

(2012) BMC Syst Biol 6 Suppl 2

PubMed: 23282146 | PubMedCentral: PMC3521187 | DOI: 10.1186/1752-0509-6-S2-S6

PDB 1st Molecule 2nd Molecule H NH 1a4y Angiogenin Ribonuclease Inhibitor 3 12 1a22 Human growth hormone Human growth hormone binding protein 7 29 1ahw Immunoglobulin Fab 5G9 Tissue factor 1 3 1brs Ba... nase Barstar 8 1 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 6 3 1cbw BPTI Trypsin inhibitor Chymotrypsin 1 4 1dan Blood coagulation factor VIIA Tissue factor 2 9 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 6 1 1fc2 Fc fragment Fragment B of protein A 1 0 1fcc Fc (IGG1) Protein G 4 2 1gc1 Envelope protein GP120 CD4 0 11 1jrh Antibody A6 Interferon-gamma receptor 8 5 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 3 6 2ptc BPTI Trypsin 1 0 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 11 6 H stands for Hot Spot and NH stands for Non-Hot Spot .

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


An analysis of B-cell epitope discontinuity.

(2012) Mol Immunol 51

PubMed: 22520973 | PubMedCentral: PMC3657695 | DOI: 10.1016/j.molimm.2012.03.030

PDB code Structural epitope a Functional epitope b Number of residues Span Number of residues Span Number of patches 1VFB 23 117 4 7 1 3HFL 21 44 2 24 1 1HFM 24 95 4 78 2 1FBI 26 89 3 77 2 1WEJ 18 102... 4 45 2 1JRH 17 53 5 5 1 a All numbers calculated by the authors.

1 Duquesnoy points out that the functional epitopes associated with three structures (PDB ID: 1VFB , 3HFL , 1JRH ) consist of a single patch located centrally within the corresponding structural epitope, whereas the functional epitopes associated with the remaining three structures (PDB ID: 1HFM , 1FBI , 1WEJ ) comprise two distinct patches.

Publication Year: 2012