Citations in PubMed

Primary Citation PubMed: 9468142 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

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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Prediction of calcium-binding sites by combining loop-modeling with machine learning.

(2009) BMC Struct Biol 9

PubMed: 20003365 | PubMedCentral: PMC2808310 | DOI: 10.1186/1472-6807-9-72

Table 1 20 apo-holo pairs of calcium-binding proteins for validation Holo structure Apo structure Loop Protein and calcium ID Protein name PDB ID Chain ID PDB ID Chain ID All RMSD (Å) Start En... RMSD (Å) Sequence 1B9AA110 PARVALBUMIN 1B9A A 1B8C A 1.48 51 62 2.68 AQDKSGFIEEDE 1C1R_247 CHYMOTRYPSIN INHIBITOR 2 1C1R A 1AZ8 A 0.60 70 80 0.13 EDNINVV E GN E 1DPO_246 TRYPSIN 1DPO A 1BRB E 0.73 70 80 0.37 E HNINVL E GN E 1DVIB275 CALPAIN 1DVI B 1AJ5 B 2.06 111 121 2.36 AG DD M E VSAT E 1DVIB277 CALPAIN 1DVI B 1AJ5 A 1.75 184 195 0.90 D T D RSGTIGSN E 1F6SB202 ALPHA-LACTALBUMIN 1F6S B 1F6R C 0.86 79 89 0.33 KFL DDD LT DD I 1HAZB1246 BETA-CASOMORPHIN-7 1HAZ B 1FLE E 1.06 70 80 0.23 E HNLNQNNGT E 1I40_305 INORGANIC PYROPHOSPHATASE 1I40 A 1MJW A 0.55 138 146 0.25 F E HYK D L E K 1K94_998 GRANCALCIN 1K94 A 1F4Q B 1.23 130 143 0.68 TVDQDGSGTV E HH E 1K94_999 GRANCALCIN 1K94 A 1F4Q A 1.35 62 72 0.67 AGQDG E V D A EE 1K96A91 S100A6 1K96 A 1K8U A 4.15 24 34 1.45 G D KHTLSKK E L 1KXQB4003 ALPHA-AMYLASE, PANCREATIC 1KXQ B 1KXV A 0.46 165 172 0.17 LL D LAL E K 1NLS_240 CONCANAVALIN A 1NLS A 1DQ0 A 0.31 9 20 0.47 L D TYPNT D IG D P 1NOL_632 HEMOCYANIN (SUBUNIT TYPE II) 1NOL A 1OXY A 0.55 577 584 0.13 V D AVSYCG 1PSH_1 PHOSPHOLIPASE A2 1PSH A 1A3D A 0.61 25 34 1.41 GCYCGRGGSG 1QMDA403 PHOSPHOLIPASE C 1QMD A 1QM6 A 0.20 265 270 0.13 SG E K D A 1QMDA405 PHOSPHOLIPASE C 1QMD A 1QM6 A 0.20 292 299 0.14 M D NPGN D F 2POR_304 PORIN 2POR A 3POR A 1.00 135 145 0.98 S D GKVG E TS ED 3LHM_131 HUMAN LYSOZYME 3LHM A 2LHM A 0.21 83 94 0.40 ALL DD NIA DD VA 5CHY_401 CHEY 5CHY A 3CHY A 0.35 55 63 0.15 IS D WNMPNM PDB ID (PDB code followed by chain identifier and calcium index) and protein names are from PDB (column 1-2).

Publication Year: 2009


A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction.

(2010) BMC Bioinformatics 11

PubMed: 20398404 | PubMedCentral: PMC2868011 | DOI: 10.1186/1471-2105-11-193

Table 1 PDB codes of the protein-ligand complexes in the three test sets HIV protease complexes ( N = 112) 1GNM , 1GNN , 1GNO , 1A30 , 1A9M , 1AAQ , 1AJV , 1AJX , 1B6J , 1B6K , 1B6L , 1B6M , 1BDQ , 1B... 7 , 1BV9 , 1BWA , 1BWB , 1C70 , 1D4K , 1D4L , 1D4Y , 1DIF , 1DMP , 1G2K , 1G35 , 1HBV , 1HEG , 1HIH , 1HII , 1HOS , 1HPO , 1HPS , 1HPV , 1HPX , 1HSH , 1HVH , 1HVI , 1HVJ , 1HVK , 1HVL , 1HVR , 1HVS , 1HWR , 1HXB , 1HXW , 1IIQ , 1IZH , 1IZI , 1LZQ , 1MES , 1MET , 1MEU , 1MRW , 1MRX , 1MSM , 1MSN , 1MTR , 1NH0 , 1ODY , 1OHR , 1PRO , 1QBR , 1QBS , 1QBT , 1QBU , 1SBG , 1SDT , 1SDU , 1SDV , 1SGU , 1SH9 , 1T7J , 1W5V , 1W5W , 1W5X , 1W5Y , 1Z1H , 1Z1R , 1ZP8 , 1ZPA , 1ZSF , 1ZSR , 2AOC , 2AOD , 2AOE , 2AQU , 2AVM , 2AVO , 2AVQ , 2AVS , 2AVV , 2BPV , 2BPY , 2BQV , 2F80 , 2F81 , 2F8G , 2FGU , 2FGV , 2HB3 , 2I0A , 2I0D , 7HVP , 7UPJ , 2HS2 , 2AOG , 2HS1 , 1A94 , 1AID , 1KZK , 1TCX , 3AID Trypsin complexes ( N = 73) 1C1R , 1C5P , 1C5Q , 1C5S , 1C5T , 1CE5 , 1F0T , 1F0U , 1K1I , 1K1J , 1K1L , 1K1M , 1K1N , 1OSS , 1PPC , 1PPH , 1QB1 , 1QB6 , 1QB9 , 1QBN , 1QBO , 1TNG , 1TNH , 1TNI , 1TNJ , 1TNK , 1TNL , 1V2J , 1V2K , 1V2L , 1V2N , 1V2Q , 1V2R , 1V2S , 1V2T , 1V2U , 1V2W , 2A31 , 2BZA , 2FX6 , 1BRA , 1G3B , 1G3C , 1G3D , 1G3E , 1GHZ , 1GI1 , 1GI4 , 1GI6 , 1GJ6 , 1J16 , 1J17 , 1O2H , 1O2J , 1O2K , 1O2N , 1O2O , 1O2Q , 1O2S , 1O2W , 1O2X , 1O2Z , 1O30 , 1O33 , 1O36 , 1O38 , 1O3D , 1O3F , 1O3H , 1O3I , 1O3J , 1O3K , 1V2O Carbonic anhydrase complexes ( N = 44) 1BN1 , 1BN3 , 1BN4 , 1BNN , 1BNQ , 1BNT , 1BNU , 1BNV , 1BNW , 1A42 , 1AVN , 1BCD , 1CIL , 1CIM , 1CIN , 1CNW , 1CNX , 1CNY , 1G1D , 1G45 , 1G46 , 1G48 , 1G4J , 1G4O , 1G52 , 1G53 , 1G54 , 1I9L , 1I9M , 1I9N , 1I9O , 1I9P , 1I9Q , 1IF7 , 1IF8 , 1OKL , 1TTM , 1XPZ , 1XQ0 , 1YDA , 1YDB , 1YDD , 2EZ7 , 2H4N In addition, a set of putative binding poses were prepared for the ligand molecule in each complex in all three test sets.

Publication Year: 2010