Citations in PubMed

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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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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


Sanjeevini: a freely accessible web-server for target directed lead molecule discovery.

(2012) BMC Bioinformatics 13 Suppl 17

PubMed: 23282245 | PubMedCentral: PMC3521208 | DOI: 10.1186/1471-2105-13-S17-S7

PDBID a Ligand (Molecular formula) EXBFE (kcal/mol)# PBFE (kcal/mol) b PBFE (kcal/mol) c 1 1BRA C 7 H 8 N 2 -2.496 -4.92 -4.59 2 1F0T C 19 H 19 N 5 O 4 S 2 -8.29 -6.92 -7.35 3 1F0U C 27 H 30 N 4 O 3 -... .89 -8.98 -6.96 4 1MTW C 26 H 28 N 4 O 3 -10.076 -7.84 -6.64 5 1PPC C 27 H 31 N 5 O 4 S -8.8 -8.46 -6.85 6 1TNH C 7 H 9 FN -4.59 -4.49 -4.28 7 1TNI C 10 H 15 N -2.32 -3.74 -3.53 8 1TNJ C 8 H 12 N -2.67 -3.72 -3.77 9 1TNK C 9 H 14 N -2.03 -3.81 -3.51 10 1TNL C 9 H 12 N -2.56 -3.56 -3.99 11 1TPP C 10 H 12 N 2 O 3 -7.95 -6.05 -5.55 12 3PTB C 7 H 8 N 2 -6.46 -5.36 -5.27 13 1S0R / 1S0Q C 8 H 10 N 3 O 1 -5.71 -5.25 -5.59 14 1S0R / 1S0Q C8H11N2O1 -6.04 -5.37 -5.51 15 1S0R / 1S0Q C7H10N3 -6.95 -5.16 -5.99 16 1S0R / 1S0Q C7H9N2 -6.35 -5.26 -5.12 17 1S0R / 1S0Q C8H11N2 -6.59 -5.33 -5.56 18 1S0R / 1S0Q C9H13N2 -6.07 -5.01 -5.41 19 1S0R / 1S0Q C10H15N2 -6.14 -5 -5.55 20 1S0R / 1S0Q C 10 H 15 N 2 (iso) -5.42 -5.26 -5.79 21 1S0R / 1S0Q C 11 H 17 N 2 -6.26 -5 -6.08 22 1S0R / 1S0Q C 12 H 19 N 2 -6.5 -5.45 -6.55 23 1S0R / 1S0Q C 13 H 21 N 2 -6.97 -5.82 -6.53 # Experimental binding free energies of trypsin binding molecules.

Publication Year: 2012