Primary Citation PubMed: 10966741
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Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity.
(2009) BMC Bioinformatics 10
PubMed: 19671127 | PubMedCentral: PMC2739202 | DOI: 10.1186/1471-2105-10-245
1F0R and 1F0S ligands shared most their chemical structures except for some minor variation for the portion of the ligands that go deep inside the P1 pocket of FXa, such that our ligand-based tool had... no problem to detect the 1F0S ligand as a one of the first hits and to correctly align it onto the query 1F0R ligand.
1F0S ligand was correctly aligned onto the query, but unfortunately, it flipped over the 2 next hits, 1NFU and 1KSN .
Publication Year: 2009
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
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