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PDB ID Mentions in PubMed Central Article count: 13

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Scoring predictive models using a reduced representation of proteins: model and energy definition.

(2007) BMC Struct Biol 7

PubMed: 17378941 | PubMedCentral: PMC1854906 | DOI: 10.1186/1472-6807-7-15

6 0.46 33.3 ig_structal 1plg 32/61 1.5 -0.2 0.57 0.0 ig_structal 1rmf 57/61 1.7 1.7 0.35 16.7 ig_structal 1tet 51/61 1.5 0.7 0.44 0.0 ig_structal 1ucb 18/61 1.6 -0.6 0.54 33.3 ig_structal 1vfa 2/61 2.... -1.6 0.33 16.7 ig_structal 1vge 31/61 3.9 -0.0 0.10 16.7 ig_structal 1yuh 61/61 1.9 2.4 0.06 33.3 ig_structal 2cgr 49/60 1.4 0.5 0.45 16.7 ig_structal 2fb4 4/61 1.7 -1.5 0.43 50.0 ig_structal 2fbj 20/61 1.4 -0.4 0.48 0.0 ig_structal 2gfb 4/61 2.0 -1.5 0.40 50.0 ig_structal 3hfl 59/61 4.2 2.7 -0.29 0.0 ig_structal 3hfm 59/61 1.6 1.9 0.38 0.0 ig_structal 6fab 29/61 1.4 -0.1 0.48 0.0 ig_structal 7fab 57/61 2.0 1.2 0.36 33.3 ig_structal 8fab 44/61 5.3 0.4 -0.01 0.0 Table 6 Performance evaluation of the energy function on ig_structal_hires decoy set Decoy set PDB id.

Publication Year: 2007


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


Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

(2008) BMC Bioinformatics 9

PubMed: 18366628 | PubMedCentral: PMC2292695 | DOI: 10.1186/1471-2105-9-148

Binding affinities Binding affinities were calculated for 5 different ligand-protein systems taken from the PDB [ 54 ] and a number of their mutants: (i) tyrosine kinase Abl in complex with imatinib (... OPJ), (ii) Tyrosyl-tRNA synthetase in complex with tyrosine (4TS1), (iii) Aspartyl-tRNA synthetase in complex with aspartate (1IL2), (iv) Lysozyme in complex with the antibody HyHel-10 (3HFM) and (v) the complex of the glycoprotein CD4 with the gp120 component of the HIV virus (1G9M).

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

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 ).

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.

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.

In our dataset of 21 cases (Table 1 ), unbound structures for both ligand and receptor molecules are only available in a few cases (1AHW, 1DFJ, 3HFM, 1JCK, 2PTC).

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

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 Δ�... 394; 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

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 ident... ty (%) 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.

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 Immunoglobulin 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.

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


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


DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions.

(2010) Nucleic Acids Res 38

PubMed: 20511591 | PubMedCentral: PMC2896140 | DOI: 10.1093/nar/gkq471

The average experimental uncertainty for 78 (PDB codes of the corresponding complexes: 1a22, 1a4y, 1bxi, 1dfj, 3hfm) of the 309 mutations amounts to 0.31 kcal mol −1 .

Publication Year: 2010


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


P-fimbriae in the presence of anti-PapA antibodies: new insight of antibodies action against pathogens.

(2013) Sci Rep 3

PubMed: 24292100 | PubMedCentral: PMC3848023 | DOI: 10.1038/srep03393

To investigate, by modeling, the binding of two arms of an IgG molecule to helical and unwound P-fimbriae, we input the atomic models of P-fimbriae 29 , PapA dimer (pdb 2UY6), an IgG (pdb 1IGT), and a... IgG Fab with bound ligand (pdb 3HFM) into UCSF Chimera software 47 .

(B) An epitope is shown at 2 nm resolution when bound to a Fab-antigen (from pdb 3HFM) shown as a ribbon diagram.

An epitope shown at 2 nm resolution is included in Fig. 6B , bound to a Fab-paratope (from pdb 3HFM).

Publication Year: 2013


Integrating water exclusion theory into ? contacts to predict binding free energy changes and binding hot spots.

(2014) BMC Bioinformatics 15

PubMed: 24568581 | PubMedCentral: PMC3941611 | DOI: 10.1186/1471-2105-15-57

Figure 3 Prediction results by β ACV ASA for the residues in the interface between Chain Y and Chain HL(together) in 3HFM.

An example of hot spot predictions We use 3HFM as a case study to illustrate the difference of the binding hot spot prediction results by β ACV ASA , FoldX and Robetta.

Publication Year: 2014