Citations in PubMed

Primary Citation PubMed: 11141566 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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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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

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 , res... lution 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

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

LigCSRre managed however to undertake some scaffolds hopping (e.g between 1E9H and 1FVV ligands), and other examples of scaffolds hopping could be cited like between 1OGU and 1H1S ligands.

Publication Year: 2009

High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations.

(2009) PLoS Comput Biol 5

PubMed: 19816553 | PubMedCentral: PMC2746282 | DOI: 10.1371/journal.pcbi.1000528

The left figure indicates the binding pocket in the CDK2-Oxindole inhibitor complex (PDB Id: 1FVV).

These structures with crystallographic resolutions of less than 3.0 Å, were retrieved from the Protein Data Bank (PDB) because the conformations of residues in the binding pocket affect the molecular docking results (PDB Id: 1C5S (trypsin) [51] , 1HWR (HIV PR) [52] , 1E66 (AChE) [53] , and 1FVV (CDK2) [46] ).

Publication Year: 2009

EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities.

(2011) Nucleic Acids Res 39

PubMed: 21051336 | PubMedCentral: PMC3013767 | DOI: 10.1093/nar/gkq878

Case study 1: identifying cyclin dependent kinases inhibitors As a test for the pharmacaphore searching routine we used the eight available structures of CDK complexes stored in the PDBbind database (... 27 ) with PDB codes 1AQ1, 1DI8, 1DM2, 1E1V, 1E1X, 1FVV, 1UNH and 2A4L.

Publication Year: 2011

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach.

(2012) Nucleic Acids Res 40

PubMed: 22649057 | PubMedCentral: PMC3394295 | DOI: 10.1093/nar/gks496

The predicted best targets are as follows: CDK2 (PDB ID: 1FVV, predicted Ki : 51.7 nM); CDK5 (PDB ID: 1UNH, predicted Ki : 71.2 nM); GSK-3β (PDB ID: 1Q41, predicted Ki : 63.3&#... 02009;nM); PDK1 (PDB ID: 2PE1, predicted Ki : 96.5 nM).

Publication Year: 2012

ReFlexIn: a flexible receptor protein-ligand docking scheme evaluated on HIV-1 protease.

(2012) PLoS One 7

PubMed: 23110159 | PubMedCentral: PMC3480487 | DOI: 10.1371/journal.pone.0048008

The last three non-binders correspond to ligands that bind to protein kinases (ligands from pdb ID's 1FMO, 1FVV, and 1JSV).

Publication Year: 2012

A structure-guided approach for protein pocket modeling and affinity prediction.

(2013) J Comput Aided Mol Des 27

PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9

PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP,... 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.

Publication Year: 2013

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4464052

Figure 6 shows a predicted pose for the 2XNB ligand (A), along with a depiction of its surface shape and electrostatic similarity to the bound pose of the ligand of 1FVV (B).

Publication Year: 2015