Primary Citation PubMed: 1304340
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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
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
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