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PDB ID Mentions in PubMed Central

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Residues crucial for maintaining short paths in network communication mediate signaling in proteins.

(2006) Mol Syst Biol 2

PubMed: 16738564 | PubMedCentral: PMC1681495 | DOI: 10.1038/msb4100063

The trypsin family of serine proteases (representative structure: 2ptc(E), bovine beta-trypsin complex with pancreatic trypsin inhibitor) Trypsin is an illustrative example of cooperative interactions... between residues belonging to different regions.

Publication Year: 2006


Identification of hot spot residues at protein-protein interface.

(2006) Bioinformation 1

PubMed: 17597870 | PubMedCentral: PMC1891667 | DOI: null

The interaction of K15 (PDB ID: BPTI, Chain I) to S190, S195 and V213 (trypsin, Chain E) is shown (PDB ID: 2PTC).

Publication Year: 2006


In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.

(2007) BMC Struct Biol 7

PubMed: 17559675 | PubMedCentral: PMC1913526 | DOI: 10.1186/1472-6807-7-37

From X-ray crystallography, two 3D-structures of the wild type BPTI-β- trypsin complex are available at 1.85 Å (PDB entry 2PTC)[ 51 ] and 1.90 Å resolution (PDB entry 3BTK) [ 2... ].

Publication Year: 2007


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

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).

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 ).

The most dramatic false negative, with ΔΔG = 10 kcal.mol -1 (Figure 1 ), corresponds to the BPTI residue K15 in the BPTI-Trypsin complex (complex PDB 2PTC ).

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.

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


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


Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

(2009) PLoS Comput Biol 5

PubMed: 19165315 | PubMedCentral: PMC2613531 | DOI: 10.1371/journal.pcbi.1000267

Structures: β -trypsin proteinase 2ptc (A), RNA-binding protein 2cjk (with the RNA chain in yellow) (B), nucleotidyltransferase 2pol (C), oxidoreductase 1leh (D).

Receptor/inhibitor pockets Three receptor/inhibitor complexes have been analyzed: 1ugh, 2ptc and 1k9o.

Publication Year: 2009


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.

The calculated RMSD values are 3.2, 2.9, 2.9, 1.6, 1.2, 3.5 and 2.2 Å for seven complexes (1AVZ, 1BRC, 1BRS, 1STF, 1TAB, 2KAI and 2PTC), for which a native-like conformation was not found, and only two complexes out of seven give the RMSD less than 2.0 Å.

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.

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

Publication Year: 2009


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


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


RASMOT-3D PRO: a 3D motif search webserver.

(2009) Nucleic Acids Res 37

PubMed: 19417073 | PubMedCentral: PMC2703991 | DOI: 10.1093/nar/gkp304

Coordinates of target and motif were extracted from beta-trypsin/BPTI complex described in PDB file 2PTC.

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

A detail of the interaction between trypsin (in grey, surface representation) and trypsin inhibitor (in red) is shown (pdb code 2PTC ).

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

Complex LZerD 3DZD+NORMAL NORMAL BSA EXVOL EXVOL +BSA 1A0O 704 11917 5320 848 5888 573 1AVW 41 26 31 958 7412 696 1AVZ 21 920 554 2237 332 77 1BQL 507 6604 294 10042 23281 935 1BRC 132 221 8657 4140 2... 35 1456 1BRS 1 3 1 20 14154 6 1BTH 1 1 1 18 10176 1 1CHO 1 1 1 534 98 97 1CSE 5 22 18 208 16286 182 1EO8 3791 7869 6472 12640 204 687 1FBI 202 4055 4004 7480 9164 1053 1FSS 26 4292 3904 204 4220 85 1GLA 1161 42275 39867 12647 1377 4074 1IAI 11 45 78 895 17448 25 1IGC 2946 5887 7988 6832 2292 1827 1JHL 2901 850 1413 8706 2191 1601 1MEL 125 30081 21657 533 3405 26 1QFU 17 54 57 2571 6279 115 1SPB 1 63 36 107 27227 4 1STF 2 13 8 101 2491 3 1TAB 20 31 40 271 2878 17 1TGS 1 1 1 426 837 11 1UGH 1 4 1 5 12311 1 2KAI 37 150 337 1750 775 374 2PTC 9 9 22 1781 12777 72 2TEC 2 536 514 9261 289 7184 2VIR 5243 18668 15018 3750 5063 9594 3HHR 351 16048 901 1332 8496 382 4HTC 1 1 1 1 17361 1 Summary Wins vs. LZerD a) - 3D+N/LZD 2/22 Normal/LZD 3/20 BSA/LZD 1/27 ExVol/LZD 4/25 E+B/LZD 6/20 Wins Overall b) 20 7 7 2 1 7 The training set included 29 bound-bound protein complexes taken from Benchmark datasets 0.0 and 1.0.

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


Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective.

(2010) BMC Bioinformatics 11

PubMed: 20462403 | PubMedCentral: PMC2882391 | DOI: 10.1186/1471-2105-11-244

Score ASA in chain ASA in complex 15 GLY 9 35.33 0.0 16 LYS 6 131.14 53.37 45 GLY 9 36.32 0.2 44 GLN 6 147.86 54.17 46 THR 7 10.97 0.0 Table 9 The conservation score and ASA (Å) information of... the unique biclique = ⟨{GLN, GLY, SER, SER, TYP},{CYS, LYS}⟩ in chain E and I of PDB entry 2PTC .

Score ASA in chain ASA in complex residues in 2PTC chain E 192 GLN 1 116.42 20.18 195 SER 9 19.16 0.0 214 SER 9 10.96 2.06 215 TRP 4 51.96 5.44 216 GLY 9 29.15 1.49 residues in 2PTC chain I 14 CYS 9 55.63 0.0 15 LYS 3 201.71 0.6 Figure 1 Examples of biclique location at the protein interfaces .

We also note that although the two chain Es in 2BTC and in 2PTC are identical chains, the specific residues involved in are not the same due to the low similarity between their partner chains.

PDB entries 1EJA :B 1TAB :I 1TGS :I 2BTC :I 2PTC :I 1BTH :P 1EJA :A A B - - - - - 1TAB :E 83 E I - - - - 1TGS :Z 83 100 Z I - - - 2BTC :E 83 100 100 E I - - 2PTC :E 83 100 100 100 E I 100 1BTH :H 37 36 36 36 36 H P The italic half is for the sequence similarity among these inhibitors, while the bold-face half is for the sequence similarity among trypsins/trypsinogen; '-' means no significant sequence alignment.

It can be seen from Table 9 that the biclique residues in have relatively small ASA in the 2PTC complex and larger ASA change upon complex formation.

As mentioned, Lys in the sequence position 15 of chain I in 2PTC is a wet-lab confirmed hot spot residue with an extremely high energy (10 kcal/mol) according to ASEdb [ 4 ].

This can be easily understood from Figure 1 : Figure 1(a) and 1(b) clearly show that the biclique residues in the biological interface 2PTC are buried.

Chain E of 1TAB , chain Z of 1TGS , chain E of 2BTC and chain E of 2PTC are identical chains.

Residue SER in 2BTC is in the position 217, while it is in the position 195 in 2PTC .

PDB entry First Chains Second Chains 1EJA -A:B GLN192-SER195-SER214-TRP215-GLY216 CYS33-LYS34 1TAB -E:I GLN192-SER214-TRP215-GLY216-SER217 CYS24-LYS26 1TGS -Z:I GLN192-SER214-TRP215-GLY216-SER217 CYS16-LYS18 2BTC -E:I GLN192-SER214-TRP215-GLY216-SER217 CYS503-LYS505 2PTC -E:I GLN192-SER195-SER214-TRP215-GLY216 CYS14-LYS15 1BTH -H:P GLN192-SER195-SER214-TRP215-GLY216 CYS14-LYS15 We take these examples to highlight that the uniqueness of DWE bicliques matches to different interfacial properties of the three types of protein interactions in terms of polarity, hydrophobicity, the composition of residues and residue pairs in protein interfaces.

For example, in Table 7 , although chain E of 2PTC and chain E of 1TAB are the identical, the occurring bicliques are involved with residues of different positions in the interaction partner chains.

For example, the conservation score of LYS15 in chain I of 2PTC is 3, but this residue contributes greatly to the formation of the complex 2PTC - its mutation results in a big binding free energy change (10 kcal/mol) according to ASEdb (Alanine Scanning Energetics database) [ 4 ].

We take in the crystal packing 2ACY in Table 8 and in the transient interaction 2PTC in Table 9 as example.

The sequence similarity among the other chains of these interactions is very low except two identical chains P in 1BTH and I in 2PTC .

Publication Year: 2010


Structure of conkunitzin-S1, a neurotoxin and Kunitz-fold disulfide variant from cone snail.

(2006) Acta Crystallogr D Biol Crystallogr 62

PubMed: 16929098 | PubMedCentral: PMC2924234 | DOI: 10.1107/S0907444906021123

Single-protein search models consisted of the Kunitz-fold proteins or domains from PDB codes 1dtx , 1tfx , 2knt and 2ptc , with N-terminal residues preceding the first cysteine and C-­terminal... residues following the final cysteine omitted.

Publication Year: 2006


Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors.

(2010) BMC Struct Biol 10

PubMed: 20961427 | PubMedCentral: PMC2974730 | DOI: 10.1186/1472-6807-10-36

Table 3 Evaluation of the success rate (ACC) of predicting IFR ensemble PDB ID Subfamily Organism TP TN FP FN ACC 1FY8 Trypsin Bos taurus 44 244 0 0 1 3TGI Trypsin Bos taurus 42 239 5 0 0.98 1TPA Tryp... in Bos taurus 44 240 1 3 0.98 3BTK Trypsin Bos taurus 43 241 1 4 0.98 3TPI Trypsin Bos taurus 43 242 1 2 0.98 2PTC Trypsin Bos taurus 44 241 0 3 0.98 2TGP Trypsin Bos taurus 45 240 0 3 0.98 4TPI Trypsin Bos taurus 44 239 1 4 0.98 2TPI Trypsin Bos taurus 44 241 1 2 0.98 1BZX Trypsin Bos taurus 43 242 2 1 0.98 1BRB Trypsin Rattus novergicus 41 236 2 2 0.98 1FAK Coagulation factor VIII Homo sapiens 44 247 6 0 0.97 1CBW Chymotrypsin Bos taurus 44 238 5 1 0.97 1MTN Chymotrypsin Bos taurus 45 239 1 3 0.98 2KAI Kallikrein Bos taurus 57 224 0 4 0.98 1EAW Matriptase MTSP1 Homo sapiens 42 241 4 1 0.98 The true positives (TP) are IFR residues present in both the native and the rigid body docked complexes.

Publication Year: 2010


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 2 Dataset 2 contains 40 complexes 1 1A0O 1EFN 1KB5 1TOC 1AGR 1FIN 1MEL 1TX4 1BRS 1FLE 1MKW 1YCS 1BTH 1FSS 1NFD 1YDR 1CBW 1GLA 1NMB 2KAI 1CHO 1GUA 1OSP 2PTC 1CSE 1HWG 1PPF 2TRC 1DHK 1IAI 1STF 3SG... 1DVF 1IGC 1TBQ 4CPA 1EBP 1JHL 1TGS 4HTC 1.

Publication Year: 2010


SdPI, the first functionally characterized Kunitz-type trypsin inhibitor from scorpion venom.

(2011) PLoS One 6

PubMed: 22087336 | PubMedCentral: PMC3210814 | DOI: 10.1371/journal.pone.0027548

To further examine the inhibition assay results, molecular dynamics (MD) simulation was employed to probe the stability of a proposed SdPI-trypsin complex model, in which the SdPI was set up to adopt ... similar position to BPTI in the complex with trypsin (PDB accession code 2PTC).

The structure of trypsin was extracted from the BPTI-trypsin complex (PDB code: 2PTC).

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.

Crystal structures for proteins, Trypsin and BPTI, are available in both bound (Trypsin/BPTI, PDB : 2PTC) and unbound (Trypsin, PDB : 5PTP; BPTI, PDB : 1BPI) forms, which provide us an opportunity to further evaluate our BD approach.

Publication Year: 2012


Role of Intrapancreatic SPINK1/Spink3 Expression in the Development of Pancreatitis.

(2012) Front Physiol 3

PubMed: 22586407 | PubMedCentral: PMC3345944 | DOI: 10.3389/fphys.2012.00126

The 3-D structures of SPINK1, BPTI, and PRSS1 were downloaded from Protein Data Bank (accession number: SPINK1, 1cgj; BPTI, 2ptc, and PRSS1, 2ra3).

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

(b) The interface between a beta-trypsin (EC number: 3.4.21.4) and its inhibitor ([PDB: 2PTC ], resolution: 1.9 Å, wetness: 0.029, rWBL: 0.954).

Publication Year: 2012


Atypical reactive center Kunitz-type inhibitor from the sea anemone Heteractis crispa.

(2012) Mar Drugs 10

PubMed: 22851925 | PubMedCentral: PMC3407930 | DOI: 10.3390/md10071545

Crystal structure of trypsin and α-chymotrypsin were extracted from 2PTC [ 63 ] and 1CBW [ 64 ] PDB files, respectively.

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