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MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.
(2008) BMC Bioinformatics 9
PubMed: 18402678 | PubMedCentral: PMC2373571 | DOI: 10.1186/1471-2105-9-184
For example we evaluated the ratio Volume of the ligand/Volume of the pocket using Q-SiteFinder [ 40 ] to be 0.95 for FX 1f0r .
Crystal structures of estrogen receptor (ER, PDB code 3ert , resolution 1.90 Å), thymidine kinase (TK, PDB code 1kim , resolution 2.14 Å), coagulation factor X (FX, PDB code 1f0r , resolution 2.10 Å), ribonuclease A (RNAse, PDB code 1afk , resolution 1.70 Å), neuraminidase (NA, PDB code 1b9s , resolution 2.50 Å), CDK2 (CDK, PDB code 1fvv , resolution 2.80 Å), and carboxypeptidase A (CBXpe, PDB code 1hdq , resolution 2.30 Å) were selected for the VLS experiments.
Publication Year: 2008
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.
PubMed: 18925937 | PubMedCentral: PMC2588602 | DOI: 10.1186/1471-2105-9-438
Dataset preparation Compound collections Energy minimization with AMMOS and the Tff and MMFF94s force fields was carried out initially on 4 small molecules, taken from several X-ray protein-ligand com... lexes in the Protein Data Bank (PDB) [ 54 ], namely: raloxifene (an inhibitor of estrogen receptor, PDB code 1err ); 4-(n-acetylamino)-3- [n-(2-ethylbutanoylamino)]benzoic acid ( FDI) (an inhibitor of neuraminidase, PDB code 1b9s ); thymidine (an inhibitor of thymidine kinase, PDB code 1kim ); thieno [3,2-b]pyridine-2-sulfonic acid [2-oxo-1-(1h-pyrrolo[2,3-c]pyridin-2-ylmethyl)- pyrrolidin-3-yl]-amide ( PR2) (an inhibitor of coagulation factor X, PDB code 1f0r ).
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.
On the contrary, 1KSN and 1NFU ligands do not share chemical features with 1F0R ligand, different groups interacting with the P1 pocket, different linker, and different group interacting with the entrance of the binding site (exposed to the solvent).
The query molecule on Figure 1 was extracted from PDB structure 1F0R .
LigCSRre managed to identify the global structural feature of the compounds, that is, a haliphatic ring surrounded by two ring-based arms and used it to superimpose the 3 FXA hits onto 1F0R .
So, any ligand-based tool cannot rely on a strong chemical similarity or even topological similarity to proceed to an accurate similarity detection between the query 1F0R ligand and 1KSN , 1NFU ligands.
Publication Year: 2009
Optimal assignment methods for ligand-based virtual screening.
(2009) J Cheminform 1
PubMed: 20150995 | PubMedCentral: PMC2820492 | DOI: 10.1186/1758-2946-1-14
target number actives number decoys number clusters a PDB code b ace c 46 1796 19 p 1o86 ache d 100 3859 18 1eve cdk2 e 47 2070 32 1ckp cox2 f 212 12606 44 1cx2 egfr g 365 15560 40 1m17 fxa h 64 2092 ... 9 1f0r hivrt i 34 1494 17 1rt1 inha j 57 2707 23 1p44 p38 k 137 6779 20 1kv2 pde5 l 26 1698 22 1xp0 pdgfrb m 124 5603 22 1t46 src n 98 5679 21 2src vegfr2 o 48 2712 31 1fgi Overview of the used data sets containing the number of actives, decoys, different chemotype clusters, and the PDB code of the complexed crystal structure which contains the search query.
Application of 3D Zernike descriptors to shape-based ligand similarity searching.
PubMed: 20150998 | PubMedCentral: PMC2820497 | DOI: 10.1186/1758-2946-1-19
Target PDB Actives Decoys Decoys per active angiotensin-converting enzyme (ace) 1o86 46 1796 39.04 acetylcholinesterase (ache) 1eve 100 3859 38.59 cyclin-dependent kinase 2(cdk2) 1ckp 47 2070 44.04 cy... looxygenase-2(cox2) 1cx2 212 12606 59.46 epidermal growth factor receptor(egfr) 1m17 365 15560 42.63 factor Xa(fxa) 1f0r 64 2092 32.69 HIV reverse transcriptase(hivrt) 1rt1 34 1494 43.94 enoyl ACP reductase(inha) 1p44 57 2707 47.49 P38 mitogen activated protein(p38) 1kv2 137 6779 49.48 phosphodiesterase(pde5) 1xp0 26 1698 65.31 platelet derived growth factor receptor kinase(pdgfrb) 1t46 124 5603 45.19 tyrosine kinase SRC(src) 2src 98 5679 57.95 vascular endothelial growth factor receptor(vegfr2) 1fgi 48 2712 56.5 The third dataset from the National Cancer Institute (NCI) consists of 42,687 compounds derived from an assay measuring protection from HIV-1 infection of human CEM cells [ 57 ].
Binding-site assessment by virtual fragment screening.
(2010) PLoS One 5
PubMed: 20404926 | PubMedCentral: PMC2852417 | DOI: 10.1371/journal.pone.0010109
Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) ACE 1uze 0.60 HIVRT 1vrt 1.66 1o86 0.17 0.37 0.4... 1rt1 1.51 2.45 1.75 1uzf 0.35 0.79 0.69 1c1c a 1.88 3.12 1.61 Alr2 1ah0 1.42 1rth a 1.62 2.28 1.61 1ah3 a 1.06 3.19 1.27 HMGR 1hw8 1.39 2acr a , b 0.88 1.72 1.10 1hwk 0.61 1.49 1.31 CDK2 1aq1 a 1.32 NA 1a4g 0.57 1buh a , b 1.77 3.20 1.44 1a4q a 0.48 2.11 0.52 1dm2 a 1.75 4.49 1.62 1nsc a 0.34 1.49 0.52 COX-2 1cvu 1.51 P38 MAPK 1a9u 1.00 1cx2 a 1.24 3.78 1.53 1kv1 3.84 10.41 1.16 3pgh a 1.11 3.96 1.64 1kv2 3.54 11.26 1.61 DHFR 3dfr 1.01 PDE5 1xoz 1.18 6dfr b 1.47 1.96 1.02 1xp0 0.79 2.23 1.24 ER 1l2i 1.69 PPARg 1fm6 1.46 3ert a 2.61 4.47 1.55 1fm9 a 1.47 4.64 1.62 1err a 2.01 4.39 1.61 2prg a 0.71 1.27 1.43 Fxa 1f0r 1.64 Thrombin 1ba8 1.53 1fjs 1.09 2.57 1.59 1hgt b 0.69 1.85 1.55 1ksn a 0.67 1.65 1.59 TK 1kim a 1.58 1xka a 1.27 2.46 1.56 1ki4 a 1.78 2.90 1.40 RMSD ave was defined as the sidechain RMSD based on binding site residues within a cutoff distance of 4.5 Å from crystallographic ligands; RMSD max is defined as the largest sidechain RMSD value among all the binding site residues.
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.
Improving structural similarity based virtual screening using background knowledge.
(2013) J Cheminform 5
PubMed: 24341870 | PubMedCentral: PMC3928642 | DOI: 10.1186/1758-2946-5-50
Table 2 Overview of the used DuD data sets Protein PDB code Ligands Decoys Protein class minsup fp_length HMGR [PDB:1HW8] 35 1242 other enzyme 0.9 66 ER [PDB:3ERT] 39 1399 nuclear hormone receptor 0.7... 62 PPAR γ [PDB:1FM9] 81 2910 nuclear hormone receptor 0.96 90 P38 MAP [PDB:1KV2] 234 8399 kinase 0.83 57 TK [PDB:1KIM] 22 785 kinase 0.9 74 FXa [PDB:1F0R] 142 5102 serine protease 0.8 81 ADA [PDB:1STW] 23 822 metalloenzyme 0.8 70 DHFR [PDB:3DFR] 201 7150 folate enzyme 0.8 70 AChE [PDB:1EVE] 105 3732 other enzyme 0.77 93 COX-2 [PDB:1CX2] 349 12491 other enzyme 0.6 65 Overview of the used DuD data sets.
Publication Year: 2013
PubMed ID is not available.
Published in 2015
The two-body contacts are calculated using non-redundant database and conformational ensembles generated from MD and MC simulations respectively ( 1A4V , 1CD3, 1F0R, 1MVF and α-synuclein) with... a distance cutoff of 8 Å.
The three dimensional structures of the ordered regions of 1CD3, 1F0R and 1MVF are obtained from the PDB, while missing residues in the disordered regions are modeled with MODELLER 39 using inputs from the protein sequence and structure of the ordered regions.
Disordered proteins are selected from two classes: (i) 1CD3, 1F0R and 1MVF , with well-defined secondary structure coexisting with highly flexible disordered regions (ii) α-synuclein, which lacks well-defined tertiary structures and is completely disordered.
Publication Year: 2015
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