Citations in PubMed

Primary Citation PubMed: 7634078 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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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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


A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.

(2008) Adv Appl Bioinform Chem 1

PubMed: 21918604 | PubMedCentral: PMC3169939 | DOI: null

Appendix B The protein databank (PDB) identifier list of the basic protein set is: 1a28, 1a42, 1a4g, 1a4q, 1abe1, 1abe2, 1abf1, 1abf2, 1aco, 1ai5, 1aoe, 1apt, 1apu, 1aqw, 1atl, 1b58, 1b9v, 1bma, 1byb,... 1byg, 1c1e, 1c5c, 1c83, 1cbs, 1cbx, 1cdg, 1ckp, 1com, 1coy, 1cps, 1cvu, 1d0l, 1d3h, 1dd7, 1dg5, 1dhf, 1dog, 1dr1, 1ebg, 1eed, 1ejn, 1epb, 1epo, 1ets, 1f0r, 1f0s, 1f3d, 1fen, 1fkg, 1fki, 1fl3, 1glp, 1hdc, 1hfc, 1hos, 1hpv, 1hsb, 1hsl, 1htf1, 1htf2, 1hyt, 1ida, 1ivb, 1jap, 1lah, 1lcp, 1lic, 1lna, 1lst, 1mdr, 1mld, 1mmq, 1mrg, 1mts, 1mup, 1nco, 1ngp, 1nis, 1okl, 1pbd, 1phd, 1phg, 1poc, 1ppc, 1pph, 1pso, 1qbr, 1qbu, 1qpq, 1rds, 1rne, 1rnt, 1rob, 1snc, 1srj, 1tlp, 1tmn, 1tng, 1tnh, 1tni, 1tnl, 1tyl, 1xid, 1xie, 1yee, 2aad, 2ack, 2ada, 2cht, 2cmd, 2cpp, 2ctc, 2fox, 2gbp, 2ifb, 2pk4, 2qwk, 2tmn, 3cla, 3cpa, 3erd, 3ert, 3tpi, 4lbd, 4phv, 5abp1, 5abp2, 5cpp, 5er1, 6rnt, and 7tim.

Publication Year: 2008


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


Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation.

(2012) Pharmaceuticals (Basel) 5

PubMed: 24281257 | PubMedCentral: PMC3816655 | DOI: 10.3390/ph5101064

PDB ID Protein 1abe L-ARABINOSE-BINDING PROTEIN 1abf L-ARABINOSE-BINDING PROTEIN 1apu ACID PROTEINASE (PENICILLOPEPSIN) 1dbb FAB' FRAGMENT 1dbj FAB' FRAGMENT 1dog GLUCOAMYLASE 1dwb THROMBIN 1epo ENDOT... IA ASPARTIC PROTEINASE 1etr THROMBIN 1ets THROMBIN 1ett THROMBIN 1hpv HIV-1 PROTEASE 1hsl HISTIDINE-BINDING PROTEIN 1htf HIV-1 PROTEASE 1hvr HIV-1 PROTEASE 1nsd NEURAMINIDASE 1pgp 6-PHOSPHOGLUCONATE DEHYDROGENASE 1phg CYTOCHROME P450 1ppc TRYPSIN 1pph TRYPSIN 1rbp RETINOL-BINDING PROTEIN 1tng TRYPSIN 1tnh TRYPSIN 1ulb PURINE NUCLEOSIDE PHOSPHORYLASE 2cgr IGG2B (KAPPA) FAB FRAGMENT 2gbp D-GALACTOSE/D-GLUCOSE-BINDING PROTEIN 2ifb INTESTINAL FATTY ACID BINDING 2phh P-HYDROXYBENZOATE HYDROXYLASE 2r04 RHINOVIRUS 14 (HRV14) 2tsc THYMIDYLATE SYNTHASE 2ypi TRIOSE PHOSPHATE ISOMERASE 3ptb TRYPSIN 4dfr DIHYDROFOLATE REDUCTASE 5abp L-ARABINOSE-BINDING PROTEIN The structural ensembles generated from the PDB structure given by MD in explicit water were prepared as follows.

Publication Year: 2012


Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking.

(2012) Pharmaceuticals (Basel) 5

PubMed: 24281339 | PubMedCentral: PMC3816669 | DOI: 10.3390/ph5121332

Thrombin (PDB IDs: 1dwb, 1etr, 1ets and 1ett) and trypsin (PDB IDs: 1ppc, 1pph, 1tng, 1tnh and 3ptb) were selected as targets.

Publication Year: 2012