Citations in PubMed

Primary Citation PubMed: 8609606 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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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


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