Citations in PubMed

Primary Citation PubMed: 15299348 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

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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Averaged kick maps: less noise, more signal... and probably less bias.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19690370 | PubMedCentral: PMC2733881 | DOI: 10.1107/S0907444909021933

Figure 3 AK maps derived from 100 kick maps were calculated at 3.0 Å resolution for molecular-replacement solutions of cathepsin H (PDB code 8pch ), ammodytin L ( 3dih ), stefin B tetr... mer ( 2oct ) and three other structures from the PDB ( 2ahn , 2fy2 and 1twl ), using actinidin, C. atrox phospholipase A 2 , 1thv , 1q6x and 1nde as search models.

To demonstrate the use of AK maps, we have calculated molecular-replacement solutions and maps for cathepsin H (PDB code 8pch ; Gunčar et al. , 1998 ▶ ), ammodytin L (PDB code 3dih ; D. Turk, G. Gunčar & I. Krizaj, unpublished work), stefin B (PDB code 2oct ; Jenko et al. , 2007 ▶ ) and three additional cases from the PDB, namely 2ahn (Y. Dall’Antonia, T. Pavkov, H. Fuchs, H. Breiteneder & W. Keller, unpublished work, Table 1 ▶ ), 2fy2 (Kim et al. , 2006 ▶ ) and 1twl (Southeast Collaboratory for Structural Genomics, unpublished work), using actinidin (Baker, 1980 ▶ ), Crotalus atrox phospholipase A 2 (Keith et al. , 1981 ▶ ), 1thv (Ko et al. , 1994 ▶ ), 1q6x (Cai et al. , 2004 ▶ ) and 1ude (Liu et al. , 2004 ▶ ) as search models.

Publication Year: 2009


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