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Identification of hot regions in protein-protein interactions by sequential pattern mining.
(2007) BMC Bioinformatics 8 Suppl 5
PubMed: 17570867 | PubMedCentral: PMC1892096 | DOI: 10.1186/1471-2105-8-S5-S8
Table 1 Summary of the first dataset Query protein (Swiss-Prot AC number) Protein name PDB complex (PDB entry : chain) P09372 Protein grpE 1dkg :A P48052 Carboxypeptidase A2 precursor 1dtd :A P20936 R... s GTPase-activating protein 1 1wql :G P10824 Guanine nucleotide-binding protein G(i) 1agr :A P15153 Ras-related C3 botulinum toxin substrate 2 1ds6 :A Table 2 Summary of the second dataset, the protein-protein docking benchmark 2.0 Complex category Number of complexes Number of chains Enzyme-Inhibitor/Substrate 23 51 Antigen-bound Antibody 12 35 Antibody-Antigen 10 30 Others 39 104 Total in the dataset 72 220 Table 3 Comparing the efficiency of MAGIIC-PRO and ConSurf Query protein (PDB Code:Chain ID) MAGIIC-PRO (seconds) ConSurf (seconds) P09372 ( 1dkg :A) 10 590 P48052 ( 1dtd :A) 15 191 P20936 ( 1wql :G) 69 122 P10824 ( 1agr :A) 16 472 P15153 ( 1ds6 :A) 7 303 Table 4 Summary of the experimental results for the second dataset Number of tested protein chains 218 Number of patterns examined 212 Number of discovered blocks 900 Average number of blocks per protein chain 4.25 Average time used for each protein chain 11.76 seconds Number of blocks that is near interface 592 (~66%) Number of blocks that form clusters 832 (~92%) The maximum support of the patterns 100% The minimum support of the patterns 13% Average support of the patterns 66% Table 5 Clustering and interface propensities of the patterns derived for different categories of the proteins in the second dataset Complex Category Average clustering propensity Average interface propensity Original Non-redundant Original Non-redundant Enzyme-Inhibitor/Substrate 90.24% 87.54 79.24% 74.46 Antigen-bound Antibody 96.11% 93.69 66.31% 64.05 Antibody-Antigen 95.56% 92.22 57.72% 50.00 Others 92.05% 90.16 67.58% 65.53 Total average in the dataset 92.77% 89.98 68.63% 66.28 Table 6 The statistics on the block numbers of the derived patterns for 218 protein chains of the second dataset.
Figure 4 The pattern discovered for PDB chain [PDB: 1agr , chain A], where the pattern blocks are shown in sticks with different blocks plotted in distinct colors and the regulator of G-protein signaling 4 is plotted in blue backbone .
Publication Year: 2007
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
Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases.
(2010) Biol Direct 5
PubMed: 21129209 | PubMedCentral: PMC3012027 | DOI: 10.1186/1745-6150-5-66
( G ) Gα bound to RGS4, GDP and AlF 4 (transition state structure)(pdb_id: 1agr ; 2.8 Ǻ) [ 58 ].
Integrating energy calculations with functional assays to decipher the specificity of G protein-RGS protein interactions.
(2011) Nat Struct Mol Biol 18
PubMed: 21685921 | PubMedCentral: PMC3130846 | DOI: 10.1038/nsmb.2068
Methods Atomic structural models The atomic models of the RGS-domains–Gα complexes used in the calculations were taken from the following PDB entries: 1AGR (Gα i1 –RGS4... ; 2IK8 (Gα i1 –RGS16); 3C7K (Gα o –RGS16); 2IHB (Gα i3 –RGS10); 2GTP (Gα i1 –RGS1); 2ODE (Gα i3 –RGS8); 1FQJ (Gα i1/t –RGS9); 2V4Z (Gα i3 –RGS2-C106S/N184D/E191K triple mutant) 24 – 28 .
Missing short segments in 2IK8 (Gα i1 residues 112–118), 2IHB (RGS10 residues 103–113), and 2GTP (Gα i1 residues 112–118) were modeled based on the structure of Gα i1 –RGS4 (PDB id 1AGR) using the program Nest 56 and partial or missing side chains were modeled using Scap 57 .
The PDB IDs of these structures are: 1AGR (RGS4); 2IK8 (RGS16h, human RGS16); 3C7K (RGS16m, mouse RGS16); 2IHB (RGS10); 2GTP (RGS1); 2ODE (RGS8); 1FQJ (RGS9); 2V4Z (RGS2*, gain-of-function RGS2 triple mutant, see Methods).
Publication Year: 2011
A P-loop mutation in G? subunits prevents transition to the active state: implications for G-protein signaling in fungal pathogenesis.
(2012) PLoS Pathog 8
PubMed: 22383884 | PubMedCentral: PMC3285607 | DOI: 10.1371/journal.ppat.1002553
A superimposition of Gα i1 (G42R)/KB-752 and the Gα i1 /RGS4 complex (PDB 1AGR; not shown) indicated that the mutant arginine side chain likely directly perturbs the RGS-binding surfac... .
Publication Year: 2012
EBs recognize a nucleotide-dependent structural cap at growing microtubule ends.
(2012) Cell 149
PubMed: 22500803 | PubMedCentral: PMC3368265 | DOI: 10.1016/j.cell.2012.02.049
(C) Structure of the heterotrimeric G protein G iα1 (PDB 1AGR) (cyan) complexed with Mg.GDP.AlF 4 (ball and stick) bound to its GAP RGS4 (rainbow-colored ribbons) ( Tesmer et al., 1997... ).
G protein activation without a GEF in the plant kingdom.
(2012) PLoS Genet 8
PubMed: 22761582 | PubMedCentral: PMC3386157 | DOI: 10.1371/journal.pgen.1002756
(C) Predicted structures of OsRGA1 (green) overlayed on Rattus norvegicus Gα i1 and RGS4 (cyan and yellow, PDB: 1AGR  ).
Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif?
(2012) PLoS One 7
PubMed: 23028656 | PubMedCentral: PMC3444507 | DOI: 10.1371/journal.pone.0044879
The PDB codes of other structures shown are 1SVS, 1AGR, 1AS0, 1AS2, 1AS3, 1BH2, 1BOF, 1CIP, 1GDD, 1GFI, 1GG2, 1GIA, 1GIL, 1GIT, 1GP2, 1KJY, 1SVK, 1Y3A, 2EBC, 2G83, 2GTP, 2HLB, 2IK8, 2OM2, 2PZ2, 2PZ3, ... XNS, 2ZJY, 2ZJZ, 3D7M, 3FFA, 3FFB and 3ONW.
Collective variable approaches for single molecule flexible fitting and enhanced sampling.
(2014) Chem Rev 114
PubMed: 24446720 | PubMedCentral: PMC3983124 | DOI: 10.1021/cr4005988
Copyright 2013 John Wiley & Sons, Inc. Figure 3 MD and TAMD simulation data for RGS4 runs with initial coordinates from PDB code 1AGR.
Publication Year: 2014
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