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Multiple Structures for Virtual Ligand Screening: Defining Binding Site Properties-Based Criteria to Optimize the Selection of the Query
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199802)19:3<319::aid-jcc6>3.0.co;2-wopenalex-snapshot
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inferredcites →https://doi.org/10.1016/j.cbpa.2004.05.001openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.jmgm.2010.10.007openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
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inferredcites →https://doi.org/10.1111/j.1747-0285.2005.00327.xopenalex-snapshot
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What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527808694.ch1openalex-snapshot
New Trends in Drug Discovery
inferred← citeshttps://doi.org/10.1002/jmr.2471openalex-snapshot
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
inferred← citeshttps://doi.org/10.1002/minf.201600043openalex-snapshot
The Art of Compiling Protein Binding Site Ensembles
inferred← citeshttps://doi.org/10.1002/minf.201700020openalex-snapshot
Discriminating Agonist from Antagonist Ligands of the Nuclear Receptors Using Different Chemoinformatics Approaches
inferred← citeshttps://doi.org/10.1007/978-94-017-9257-8_15openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-015-9877-9openalex-snapshot
Statistical analysis of EGFR structures’ performance in virtual screening
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12313-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/bs.armc.2022.08.006openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.biochi.2017.10.003openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bioorg.2018.11.030openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bpc.2021.106593openalex-snapshot
In silico drug discovery for a complex immunotherapeutic target - human c-Rel protein
inferred← citeshttps://doi.org/10.1016/j.drudis.2013.10.027openalex-snapshot
Modelling three-dimensional protein structures for applications in drug design
inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.01.054openalex-snapshot
New selective cyclooxygenase-2 inhibitors from cyclocoumarol: Synthesis, characterization, biological evaluation and molecular modeling
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.11.015openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.chemrestox.4c00455openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00511openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00848openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00090openalex-snapshot
Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00588openalex-snapshot
SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00684openalex-snapshot
Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00283openalex-snapshot
Screening Explorer–An Interactive Tool for the Analysis of Screening Results
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00314openalex-snapshot
Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles
inferred← citeshttps://doi.org/10.1021/ci500305copenalex-snapshot
Importance of the Pharmacological Profile of the Bound Ligand in Enrichment on Nuclear Receptors: Toward the Use of Experimentally Validated Decoy Ligands
inferred← citeshttps://doi.org/10.1021/ci500406kopenalex-snapshot
Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes
inferred← citeshttps://doi.org/10.1021/ct500381copenalex-snapshot
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
inferred← citeshttps://doi.org/10.1021/jm500132popenalex-snapshot
NRLiSt BDB, the Manually Curated Nuclear Receptors Ligands and Structures Benchmarking Database
inferred← citeshttps://doi.org/10.1080/07391102.2015.1073632openalex-snapshot
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inferred← citeshttps://doi.org/10.18632/oncotarget.25966openalex-snapshot
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inferred← citeshttps://doi.org/10.2174/1568026614666140929124445openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fendo.2022.986016openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fphar.2018.00011openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/cells8111431openalex-snapshot
Hits Discovery on the Androgen Receptor: In Silico Approaches to Identify Agonist Compounds
inferred← citeshttps://doi.org/10.3390/ijms22062846openalex-snapshot
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inferred← citeshttps://doi.org/10.4155/fmc.15.150openalex-snapshot
Sampling of Conformational Ensemble for Virtual Screening Using Molecular Dynamics Simulations and Normal Mode Analysis
inferred← citeshttps://doi.org/10.70675/2b288725z2446z48c5z833ezf53915cd324bopenalex-snapshot
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