Primary Citation PubMed: 3463986
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Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble.
(2010) J Comput Aided Mol Des 24
PubMed: 20499135 | PubMedCentral: PMC2901495 | DOI: 10.1007/s10822-010-9365-1
Two structures (1RO9 and 3CPA) were removed from the list, because of questionable B-factors [ 16 ].
Publication Year: 2010
Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.
(2011) PLoS One 6
PubMed: 21799754 | PubMedCentral: PMC3143127 | DOI: 10.1371/journal.pone.0021875
g005 Figure 5 Comparison of the HxxE motifs in carboxypeptidase A [(A), PDB code 3cpa)] and PIBO [(B), PDB code 3n8u)].
Publication Year: 2011
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
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
The target proteins were the macrophage migration inhibitory factor (PDB code: 1gcz), COX-2 (PDB code: 1cx2, 1pxx, 3pgh, 4cox and 6cox), HIV protease-1 (PDB code: 1aid, 1hpx and 1ivp), thermolysin (PD... code: 1tmn, 2tmn, 1tlp), and GST (PDB code: 18gs, 2gss, and 3pgt), and carboxypeptidase A (PDB code: 1cbx, 1cps, 3cpa).
Publication Year: 2012
The Protein Data Bank archive as an open data resource.
(2014) J Comput Aided Mol Des 28
PubMed: 25062767 | PubMedCentral: PMC4196035 | DOI: 10.1007/s10822-014-9770-y
Early structures included myoglobin ( 1 PDB ID 1mbn [ 6 , 7 ]), the first structure solved by X-ray crystallography, and small enzymes ( 2 top 4pti [ 48 ], bottom right 2cha [ 49 ], bottom left 3cpa [... 50 ]).
Publication Year: 2014
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