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PDB ID Mentions in PubMed Central Article count: 3

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PDB ID Mentions in PubMed Central

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Modeling of loops in proteins: a multi-method approach.

(2010) BMC Struct Biol 10

PubMed: 20149252 | PubMedCentral: PMC2837870 | DOI: 10.1186/1472-6807-10-5

loop length PDB codes and loop ranges 4 7rsa 47-50, 4gcr 116-119, 2tgi 72-75, 2exo 161-164, 1xif 82-85, 1tml 42-45, 1tib 46-49, 1thw 194-197, 1rcf 111-114, 1ppn 42-45, 1plc 74-77, 1pbe 117-120, 1nfp 3... -40, 1frd 59-62, 1cbs 21-24, 1ads 99-102, 1aaj 82-85 5 7rsa 75-79, 2hbg 37-41, 2cmd 188-192, 1vcc 63-67, 1tml 147-151, 1tca 157-161, 1sbp 181-185, 1prn 187-191, 1noa 88-92, 1nfp 95-99, 1nar 56-60, 1kuh 37-41, 1hbq 158-162, 1hbg 19-23, 1frd 83-87, 153l 131-135 6 5p21 104-109, 3pte 256-261, 3pte 131-136, 2ayh 81-86, 1tca 94-99, 1tca 38-43, 1rge 73-78, 1noa 25-30, 1mrp 233-238, 1gca 100-105, 1ede 180-185, 1cbs 66-71, 1brt 253-258, 1brt 174-179, 1ads 150-155, 1ads 149-154 7 5p21 83-89, 2pth 95-101, 1tml 20-26, 1tca 132-138, 1php 135-141, 1mbd 17-23, 1lif 64-70, 1iab 142-148, 1hbg 46-52, 1gca 196-202, 1edg 309-315, 1dad 116-122, 1brt 226-232, 1bkf 64-70, 1ads 186-192 8 2ayh 194-201, 1tml 187-194, 1thw 18-25, 1prn 150-157, 1nwp 84-91, 1nls 97-104, 1nar 192-199, 1hbq 31-38, 1arb 136-143, 1alc 34-41, 1ads 274-281 9 3pte 107-115, 2ayh 169-177, 1xnb 133-141, 1xnb 116-124, 1php 91-99, 1nls 131-139, 1ede 257-265, 1arb 168-176, 1aac 58-66 10 7rsa 87-96, 7rsa 33-42, 7rsa 110-119, 2cmd 57-66, 1whi 47-56, 1tca 23-32, 1scs 65-74, 1ppn 190-199, 1plc 42-51, 1mrj 173-182, 1ixh 84-93, 1gvp 49-58, 1fkf 63-72, 1arb 41-50, 1amp 181-190, 1ads 171-180, 1ads 170-179, 135l 18-27 11 3pte 91-101, 2pth 8-18, 1rcf 122-132, 1ixh 120-130, 1dad 42-52, 153l 154-164 12 2ayh 21-32, 1ixh 160-171, 1bkf 9-20, 1arb 74-85, 153l 98-109 16 1tml 73-88, 1tml 219-234, 1tca 184-199, 1rge 37-52, 1prn 106-121, 1nar 10-25, 1iab 136-151, 1frd 33-48, 1edg 233-248, 1edg 167-182, 1brt 57-72, 1amp 98-113, 1ads 210-225 18 1tml 73-90, 1tml 219-236, 1tca 184-201, 1prn 106-123, 1nar 10-27, 1iab 136-153, 1byt 807-824, 1byt 700-717, 1byt 359-376, 1byt 230-247, 1bst 57-74, 1bst 129-146, 1b57 209-226, 1awj 2-19, 1amp 98-115, 1ahj 101-118, 1ads 210-227, 1acc 36-53, 1acc 183-200 20 1br4 390-409, 1br4 349-368, 1br4 291-310, 1br2 246-265, 1azx 362-381 22 1tml 219-240, 1prn 106-127, 1nar 10-31, 1kk7 291-312, 1jez 117-138, 1itk 179-200, 1itk 157-178, 1e04 351-372, 1clq 380-401, 1br4 71-92, 1br4 256-277, 1b3k 322-343, 1aoa 182-203 23 1nfb 253-275, 1lzj 2-24, 1izl 21-43, 1i50 46-68, 1dzg 367-389 24 1uoz 224-247, 1mnd 277-300, 1miu 93-116, 1i19 415-438, 1hfb 86-109 25 2hs0 319-343, 2gah 437-461, 2fqf 293-317, 2e4y 311-335, 1zba 16-40, 1tml 219-243, 1qme 127-151, 1prn 106-130, 1kmh 117-141, 1eah 247-271, 1dms 596-620, 1dhx 376-400, 1dhx 11-35 Using MODELLER, we generated 500 examples of individual loop regions, which were subsequently ranked by the DOPE statistical potential [ 22 ].

Publication Year: 2010


Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

(2010) BMC Struct Biol 10 Suppl 1

PubMed: 20487510 | PubMedCentral: PMC2873826 | DOI: 10.1186/1472-6807-10-S1-S3

Table 1 The correlation coefficients between the experimental and calculated B-factors using different models Protein R(Å) ANM GNM STeM Protein R(Å) ANM GNM STeM Protein R(Å) A... M GNM STeM 1AAC 1.31 0.7 0.71 0.76 1ADS 1.65 0.77 0.74 0.71 1AHC 2.00 0.79 0.68 0.61 1AKY 1.63 0.56 0.72 0.6 1AMM 1.20 0.56 0.72 0.55 1AMP 1.80 0.62 0.59 0.68 1ARB 1.20 0.78 0.76 0.83 1ARS 1.80 0.14 0.43 0.41 1ARU 1.60 0.7 0.78 0.79 1BKF 1.60 0.52 0.43 0.5 1BPI 1.09 0.43 0.56 0.57 1CDG 2.00 0.65 0.62 0.71 1CEM 1.65 0.51 0.63 0.76 1CNR 1.05 0.34 0.64 0.42 1CNV 1.65 0.69 0.62 0.68 1CPN 1.80 0.51 0.54 0.56 1CSH 1.65 0.44 0.41 0.57 1CTJ 1.10 0.47 0.39 0.62 1CUS 1.25 0.74 0.66 0.76 1DAD 1.60 0.28 0.5 0.42 1DDT 2.00 0.21 -0.01 0.49 1EDE 1.90 0.67 0.63 0.75 1EZM 1.50 0.56 0.6 0.58 1FNC 2.00 0.29 0.59 0.61 1FRD 1.70 0.54 0.83 0.77 1FUS 1.30 0.4 0.63 0.61 1FXD 1.70 0.58 0.56 0.7 1GIA 2.00 0.68 0.67 0.69 1GKY 2.00 0.36 0.55 0.44 1GOF 1.70 0.75 0.76 0.78 1GPR 1.90 0.65 0.62 0.66 1HFC 1.50 0.63 0.38 0.35 1IAB 1.79 0.36 0.42 0.53 1IAG 2.00 0.34 0.52 0.44 1IFC 1.19 0.61 0.67 0.53 1IGD 1.10 0.18 0.44 0.27 1IRO 1.10 0.82 0.51 0.85 1JBC 1.15 0.72 0.7 0.73 1KNB 1.70 0.63 0.66 0.54 1LAM 1.60 0.53 0.63 0.71 1LCT 2.00 0.52 0.57 0.61 1LIS 1.90 0.16 0.43 0.3 1LIT 1.55 0.65 0.62 0.76 1LST 1.80 0.39 0.72 0.73 1MJC 2.00 0.67 0.67 0.61 1MLA 1.50 0.59 0.57 0.54 1MRJ 1.60 0.66 0.49 0.5 1NAR 1.80 0.62 0.76 0.74 1NFP 1.60 0.23 0.48 0.41 1NIF 1.70 0.42 0.58 0.61 1NPK 1.80 0.53 0.55 0.64 1OMP 1.80 0.61 0.63 0.65 1ONC 1.70 0.55 0.7 0.58 1OSA 1.68 0.36 0.42 0.55 1OYC 2.00 0.78 0.73 0.77 1PBE 1.90 0.53 0.61 0.63 1PDA 1.76 0.6 0.76 0.58 1PHB 1.60 0.56 0.52 0.59 1PHP 1.65 0.59 0.63 0.65 1PII 2.00 0.19 0.44 0.28 1PLC 1.33 0.41 0.47 0.42 1POA 1.50 0.54 0.66 0.42 1POC 2.00 0.46 0.52 0.39 1PPN 1.60 0.61 0.64 0.67 1PTF 1.60 0.47 0.6 0.54 1PTX 1.30 0.65 0.51 0.62 1RA9 2.00 0.48 0.61 0.53 1RCF 1.40 0.59 0.63 0.58 1REC 1.90 0.34 0.5 0.49 1RIE 1.50 0.71 0.25 0.52 1RIS 2.00 0.25 0.24 0.47 1RRO 1.30 0.08 0.31 0.36 1SBP 1.70 0.69 0.72 0.67 1SMD 1.60 0.5 0.62 0.67 1SNC 1.65 0.68 0.71 0.72 1THG 1.80 0.5 0.53 0.5 1TML 1.80 0.64 0.64 0.58 1UBI 1.80 0.56 0.69 0.61 1WHI 1.50 0.12 0.33 0.38 1XIC 1.60 0.29 0.4 0.47 2AYH 1.60 0.63 0.73 0.82 2CBA 1.54 0.67 0.75 0.8 2CMD 1.87 0.68 0.6 0.62 2CPL 1.63 0.61 0.6 0.72 2CTC 1.40 0.63 0.67 0.75 2CY3 1.70 0.51 0.5 0.67 2END 1.45 0.63 0.71 0.68 2ERL 1.00 0.74 0.73 0.85 2HFT 1.69 0.63 0.79 0.72 2IHL 1.40 0.62 0.69 0.72 2MCM 1.50 0.78 0.83 0.79 2MHR 1.30 0.65 0.52 0.64 2MNR 1.90 0.46 0.5 0.47 2PHY 1.40 0.54 0.55 0.68 2RAN 1.89 0.43 0.4 0.31 2RHE 1.60 0.28 0.38 0.33 2RN2 1.48 0.68 0.71 0.75 2SIL 1.60 0.43 0.5 0.51 2TGI 1.80 0.69 0.71 0.73 3CHY 1.66 0.61 0.75 0.68 3COX 1.80 0.71 0.71 0.72 3EBX 1.40 0.22 0.58 0.4 3GRS 1.54 0.44 0.57 0.59 3LZM 1.70 0.6 0.52 0.66 3PTE 1.60 0.68 0.83 0.77 4FGF 1.60 0.41 0.27 0.43 4GCR 1.47 0.73 0.81 0.75 4MT2 2.00 0.42 0.37 0.46 5P21 1.35 0.4 0.51 0.45 7RSA 1.26 0.42 0.63 0.59 8ABP 1.49 0.61 0.82 0.62 Column R(Å) gives the resolution of each structure.

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