Citations in PubMed

Primary Citation PubMed: 8784355 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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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.

Publication Year: 2008


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


Single domain antibodies: promising experimental and therapeutic tools in infection and immunity.

(2009) Med Microbiol Immunol 198

PubMed: 19529959 | PubMedCentral: PMC2714450 | DOI: 10.1007/s00430-009-0116-7

b Chicken lysozyme in complex with an inhibitory camel sdAb (pdb code 1mel).

Publication Year: 2009


Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.

(2009) Nat Struct Mol Biol 16

PubMed: 19543291 | PubMedCentral: PMC2722044 | DOI: 10.1038/nsmb.1619

( c ) Structure of the complex between the camel single-domain V H antibody cAb-Lys3 (violet) and HEL (green) (Protein Data Bank accession code 1MEL).

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


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