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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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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.

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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

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 - - 1... GU 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


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

(2009) BMC Bioinformatics 10

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

PDB a) Class b) Difficulty c) #Atoms (R, L) d) ΔASA (Å 2 ) e) 3DZD Correlation for Bound interface 3DZD Correlation for Unbound interface 1AY7 ( 1RGH ; 1A19 ) E E 747,721 1237 0.93 0.9... 1CGI ( 2CGA ; 1HPT ) E E 1800,441 2053 0.96 0.97 2PCC ( 1CCP ; 1YCC ) E E 2339,847 1141 0.99 0.98 2SNI ( 1UBN ; 2CI2 ) E E 1932,521 1628 0.97 0.95 1ACB ( 2CGA ; 1EGL ) E MD 1799,575 1544 0.94 0.95 1AHW ( 1FGN ; 1TFH ) A E 3304,1622 1899 0.99 0.98 1FSK ( 1FSK ; 1BV1 ) A E 3347,1231 1623 0.95 0.89 1MLC ( 1MLB ; 3LZT ) A E 3290,1000 1392 0.97 0.96 1NCA ( 1NCA ; 7NN9 ) A E 3329,3067 1953 0.99 0.99 2JEL ( 2JEL ; 1POH ) A E 3297,640 1501 0.92 0.90 1KXP ( 1IJJ ; 1KW2 ) O E 2782,3527 3341 0.96 0.97 1IB1 ( 1QJB ; 1KUY ) O MD 3673,1312 2808 0.95 0.87 1WQ1 ( 6Q21 ; 1WER ) O MD 2534,1351 2913 0.92 0.93 1ATN ( 1IJJ ; 3DNI ) O D 2942,2036 1774 0.95 0.97 1DE4 ( 1A6Z ; 1CX8 ) O D 3064,1351 2066 0.98 0.97 a) The PDB IDs for the unbound proteins are shown in brackets.

Publication Year: 2009


Mutation bias favors protein folding stability in the evolution of small populations.

(2010) PLoS Comput Biol 6

PubMed: 20463869 | PubMedCentral: PMC2865504 | DOI: 10.1371/journal.pcbi.1000767

3lzt), ATP synthase epsilon chain of E.Coli (135 amino acids, PDB id.

Publication Year: 2010


Beyond rotamers: a generative, probabilistic model of side chains in proteins.

(2010) BMC Bioinformatics 11

PubMed: 20525384 | PubMedCentral: PMC2902450 | DOI: 10.1186/1471-2105-11-306

Structure L, B a Lennard-Jones b BASILISK c BASILISK BB d IRECS e SCWRL 4 e χ 1 (%) χ 2 | χ 1 (%) f χ 1 (%) χ 2 | χ 1 (%) f χ 1 (%) χ 2 ... χ 1 (%) f χ 1 (%) χ 2 | χ 1 (%) f χ 1 (%) χ 2 | χ 1 (%) f 1NAR 289, 45 77.78 76.92 73.33 87.50 93.33 87.50 84.44 70.37 86.67 79.31 5P21 166, 21 90.48 77.78 85.71 100.00 95.24 88.89 95.24 88.89 100.00 80.00 1BJ7 150, 12 91.67 75.00 100.00 77.78 100.00 77.78 91.67 75.00 83.33 85.71 1GCI 269, 40 95.00 86.67 97.50 81.25 100.00 81.25 95.00 85.71 97.50 93.33 2BAA 243, 30 86.67 60.00 83.33 86.67 90.00 82.35 86.67 81.25 90.00 94.12 1DHN 121, 15 93.33 100.00 100.00 85.71 86.67 100.00 93.33 100.00 93.33 100.00 1AMM 174, 22 90.91 100.00 100.00 92.86 100.00 92.86 100.00 85.71 86.36 90.91 1IC6 279, 47 89.36 73.68 91.49 70.00 93.62 75.00 91.49 73.68 93.62 85.00 1KOE 172, 26 80.77 92.86 73.08 84.62 80.77 84.62 92.31 92.86 88.46 84.62 2HVM 273, 43 83.72 74.07 95.35 82.76 90.70 89.66 90.70 85.19 90.70 84.62 3LZT 129, 10 80.00 83.33 70.00 83.33 80.00 83.33 100.00 83.33 100.00 83.33 1CEX 197, 24 95.83 89.47 100.00 100.00 95.83 100.00 87.50 94.74 100.00 100.00 1AGY 197, 25 92.00 84.21 96.00 100.00 96.00 100.00 84.00 94.74 92.00 100.00 1EDG 380, 76 85.53 65.85 85.53 85.00 90.79 81.82 85.53 80.49 89.47 86.05 1THV 207, 20 85.00 76.92 80.00 91.67 85.00 92.31 90.00 76.92 90.00 100.00 2CPL 164, 24 95.83 73.33 91.67 85.71 95.83 93.33 100.00 80.00 95.83 93.33 1NPK 150, 16 100.00 60.00 100.00 80.00 100.00 90.00 93.75 88.89 87.50 88.89 1MLA 305, 38 97.37 71.43 97.37 86.36 100.00 86.36 94.74 75.00 92.11 84.21 1ARB 263, 37 89.19 90.48 89.19 88.89 86.49 85.00 86.49 68.42 83.78 90.00 1MML 251, 19 78.95 81.82 84.21 75.00 89.47 91.67 94.74 83.33 94.74 91.67 1CHD 198, 26 96.15 68.75 96.15 81.25 100.00 76.47 92.31 73.33 92.31 80.00 1QQ4 198, 25 80.00 60.00 84.00 80.00 84.00 90.91 88.00 63.64 88.00 81.82 1QJ4 256, 36 83.33 75.00 91.67 81.48 94.44 81.48 91.67 85.71 94.44 81.48 1B9O 123, 14 78.57 50.00 71.43 57.14 78.57 50.00 92.86 66.67 92.86 44.44 1BYI 224, 30 80.00 86.67 100.00 100.00 96.67 94.12 90.00 87.50 93.33 100.00 1XNB 185, 22 90.91 91.67 100.00 91.67 95.45 100.00 100.00 66.67 95.45 91.67 2PTH 193, 19 94.74 100.00 100.00 100.00 94.74 100.00 94.74 100.00 100.00 100.00 1WHI 122, 12 91.67 100.00 100.00 75.00 100.00 75.00 91.67 100.00 100.00 100.00 153L 185, 26 84.62 93.33 96.15 93.33 88.46 86.67 100.00 87.50 100.00 100.00 1QTW 285, 35 94.29 84.00 91.43 91.67 91.43 83.33 88.57 70.83 97.14 80.77 2IHL 129, 12 66.67 75.00 75.00 75.00 83.33 75.00 100.00 75.00 100.00 75.00 1CZ9 139, 14 85.71 88.89 85.71 100.00 100.00 100.00 100.00 88.89 100.00 100.00 2RN2 155, 11 90.91 87.50 90.91 87.50 90.91 100.00 81.82 100.00 81.82 100.00 1RCF 169, 28 92.86 87.50 96.43 82.61 100.00 95.83 82.14 80.00 92.86 90.91 7RSA 124, 12 75.00 100.00 75.00 100.00 75.00 100.00 75.00 100.00 91.67 100.00 1A8Q 274, 39 87.18 70.00 71.79 93.75 89.74 80.95 94.87 87.50 92.31 95.65 1CEM 363, 55 89.09 64.52 83.64 77.42 94.55 79.41 89.09 80.00 89.09 80.00 1AAC 105, 13 100.00 75.00 100.00 100.00 100.00 100.00 92.31 87.50 100.00 87.50 1PLC 99, 10 100.00 85.71 90.00 66.67 100.00 71.43 90.00 85.71 100.00 71.43 1BD8 156, 11 81.82 100.00 90.91 85.71 90.91 100.00 100.00 100.00 90.91 85.71 1NLS 237, 23 78.26 85.71 86.96 87.50 86.96 81.25 86.96 80.00 91.30 81.25 1IXH 321, 44 81.82 72.00 84.09 84.62 88.64 85.19 93.18 75.00 88.64 84.00 1AKO 268, 35 77.14 72.73 85.71 91.30 85.71 91.30 100.00 81.48 97.14 88.46 Average 207, 27 87.44 80.65 89.32 86.25 92.08 87.49 91.92 83.43 93.13 88.26 The table shows the percentage of correctly predicted χ angles for the different MCMC experiments.

Publication Year: 2010


Evidence of functional protein dynamics from X-ray crystallographic ensembles.

(2010) PLoS Comput Biol 6

PubMed: 20865158 | PubMedCentral: PMC2928775 | DOI: 10.1371/journal.pcbi.1000911

Structure factor data was then calculated but without atomic relaxation of atomic positions , in order to compare the structural deviations of the MD model from the 3LZT X-ray structure reference.

The P1 space group ensemble and the non-P1 space group ensembles compared to the 3LZT-MSSA ensemble.

HEWL is unique among almost all proteins in the PDB because (1) there is at least one high resolution structure that serves as the reference (here 3LZT), (2) it contains no prosthetic groups or metals, (3) it is a protein that has been solved in multiple space groups, and (4) there are ∼80 independent solved structures to generate an experimental ensemble.

Based on this data, the experimental ensembles include: (1) the X-ray ensemble generated from multi-start simulated annealing of 3LZT (3LZT-MSSA), (2) the X-ray ensemble of HEWL structures that crystallize in the P1 space group like 3LZT, and (3) the X-ray ensemble of HEWL structures that crystallizes into alternative space groups to P1, which we refer to as the non-P1 ensemble.

For consistency the original HEWL model (3LZT) used throughout this study was re-refined in phenix.refine [36] at 1.10Å resolution, yielding a high quality structure with an R-factor = 0.0990 and R-free = 0.1308.

We quantify the structural variations on a per residue basis among the ensembles by calculating the local density correlation (LDC) coefficients of electron density values between X-ray and MD ensembles computed from the model maps around individual amino-acid residues [38] , [39] , [40] (1) where the ρ's are electron density values at grid points, and Eref and Ealt refer to densities of the members of the reference 3LZT-MSSA ensemble and the alternative ensemble to be compared, respectively.

Publication Year: 2010


Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.

(2013) PLoS One 8

PubMed: 24391900 | PubMedCentral: PMC3877219 | DOI: 10.1371/journal.pone.0084123

A similar comparison to experiment for 13 other proteins is given in Table 2 (PDB-codes: 1BRF, 1CEX, 1CY5, 1ET1, 1I27, 1IFC, 1IGD, 1OGW, 1PLC, 1RGE, 1RUV, 3LZT, 5PTI).

Publication Year: 2013


Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation.

(2014) J Chem Theory Comput 10

PubMed: 24803862 | PubMedCentral: PMC3985686 | DOI: 10.1021/ct401042b

3.4 Hen Egg White Lysozyme We used the structure solved in PDB code 3LZT as the starting structure for our simulations.

Publication Year: 2014