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Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening

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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)1097-0134(20000501)39:2<178::aid-prot8>3.0.co;2-6openalex-snapshot

Protein docking using spherical polar Fourier correlations

inferredcites →https://doi.org/10.1002/minf.201000149openalex-snapshot

Using Spherical Harmonic Surface Property Representations for Ligand‐Based Virtual Screening

inferredcites →https://doi.org/10.1007/s00894-007-0257-9openalex-snapshot

Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment

inferredcites →https://doi.org/10.1007/s00894-008-0286-zopenalex-snapshot

SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces

inferredcites →https://doi.org/10.1007/s10822-007-9163-6openalex-snapshot

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?

inferredcites →https://doi.org/10.1007/s10822-009-9302-3openalex-snapshot

Computation of 3D queries for ROCS based virtual screens

inferredcites →https://doi.org/10.1016/j.bmcl.2005.10.032openalex-snapshot

Conformationally biased P3 amide replacements of β-secretase inhibitors

inferredcites →https://doi.org/10.1016/j.ejmech.2004.10.014openalex-snapshot

Ligand-based assessment of factor Xa binding site flexibility via elaborate pharmacophore exploration and genetic algorithm-based QSAR modeling

inferredcites →https://doi.org/10.1016/j.jmb.2005.10.067openalex-snapshot

High-resolution Crystal Structure of Aldose Reductase Complexed with the Novel Sulfonyl-pyridazinone Inhibitor Exhibiting an Alternative Active Site Anchoring Group

inferredcites →https://doi.org/10.1016/j.jmb.2007.03.021openalex-snapshot

Evidence for a Novel Binding Site Conformer of Aldose Reductase in Ligand-Bound State

inferredcites →https://doi.org/10.1016/s0968-0896(98)00139-4openalex-snapshot

Molecular modeling studies of the binding modes of aldose reductase inhibitors at the active site of human aldose reductase

inferredcites →https://doi.org/10.1016/s0969-2126(97)00216-5openalex-snapshot

A ‘specificity’ pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil

inferredcites →https://doi.org/10.1021/ci050059vopenalex-snapshot

An Analytical, Variable Resolution, Complete Description of Static Molecules and Their Intermolecular Binding Properties

inferredcites →https://doi.org/10.1021/ci100263popenalex-snapshot

Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

inferredcites →https://doi.org/10.1021/ci600186bopenalex-snapshot

Prediction of Multiple Binding Modes of the CDK2 Inhibitors, Anilinopyrazoles, Using the Automated Docking Programs GOLD, FlexX, and LigandFit: An Evaluation of Performance

inferredcites →https://doi.org/10.1021/ci600426eopenalex-snapshot

Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem

inferredcites →https://doi.org/10.1021/ci7001507openalex-snapshot

Toward High Throughput 3D Virtual Screening Using Spherical Harmonic Surface Representations

inferredcites →https://doi.org/10.1021/ci700415gopenalex-snapshot

Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand−Receptor Docking

inferredcites →https://doi.org/10.1021/ci800257xopenalex-snapshot

Clustering and Classifying Diverse HIV Entry Inhibitors Using a Novel Consensus Shape-Based Virtual Screening Approach: Further Evidence for Multiple Binding Sites within the CCR5 Extracellular Pocket

inferredcites →https://doi.org/10.1021/ci800303kopenalex-snapshot

Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set

inferredcites →https://doi.org/10.1021/ci8003978openalex-snapshot

Better than Random? The Chemotype Enrichment Problem

inferredcites →https://doi.org/10.1021/ci8004226openalex-snapshot

How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information

inferredcites →https://doi.org/10.1021/ci900507gopenalex-snapshot

Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment

inferredcites →https://doi.org/10.1021/ja900616bopenalex-snapshot

Multiple Independent Binding Sites for Small-Molecule Inhibitors on the Oncoprotein c-Myc

inferredcites →https://doi.org/10.1021/jm049092jopenalex-snapshot

Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4

inferredcites →https://doi.org/10.1021/jm050382popenalex-snapshot

Naphtho[1,2-d]isothiazole Acetic Acid Derivatives as a Novel Class of Selective Aldose Reductase Inhibitors

inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot

Comparison of Shape-Matching and Docking as Virtual Screening Tools

inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm061389popenalex-snapshot

Identification of Nonpeptide CCR5 Receptor Agonists by Structure-based Virtual Screening

inferredcites →https://doi.org/10.1021/jm800914nopenalex-snapshot

Discovery and X-ray Crystallographic Analysis of a Spiropiperidine Iminohydantoin Inhibitor of β-Secretase

inferredcites →https://doi.org/10.1038/372739a0openalex-snapshot

A protein kinase involved in the regulation of inflammatory cytokine biosynthesis

inferredcites →https://doi.org/10.1038/nsb0497-311openalex-snapshot

A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket

inferredcites →https://doi.org/10.1038/nsb770openalex-snapshot

Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site

inferredcites →https://doi.org/10.1042/bj3010713openalex-snapshot

Multiple binding sites involved in the effect of choline esters on decarbamoylation of monomethylcarbamoyl- or dimethylcarbamoly-acetylcholinesterase

inferredcites →https://doi.org/10.1073/pnas.0910757106openalex-snapshot

Modulation of γ-secretase specificity using small molecule allosteric inhibitors

inferredcites →https://doi.org/10.1074/jbc.m007668200openalex-snapshot

Multiple Binding Sites in Collagen Type I for the Integrins α1β1 and α2β1

inferredcites →https://doi.org/10.1074/jbc.m302260200openalex-snapshot

X-ray Crystal Structure of the Liver X Receptor β Ligand Binding Domain

inferredcites →https://doi.org/10.1080/01621459.1963.10500845openalex-snapshot

Hierarchical Grouping to Optimize an Objective Function

inferredcites →https://doi.org/10.1093/protein/9.11.1063openalex-snapshot

An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies

inferredcites →https://doi.org/10.1111/j.1749-6632.1993.tb17149.xopenalex-snapshot

Bicyclic Imidazoles as a Novel Class of Cytokine Biosynthesis Inhibitors

inferredcites →https://doi.org/10.1124/mol.108.049775openalex-snapshot

Comparison of the Potential Multiple Binding Modes of Bicyclam, Monocylam, and Noncyclam Small-Molecule CXC Chemokine Receptor 4 Inhibitors

inferredcites →https://doi.org/10.1584/jpestics.g08-25openalex-snapshot

Design of novel carbamate acetylcholinesterase inhibitors based on the multiple binding sites of acetylcholinesterase

inferredcites →https://doi.org/10.2741/1839openalex-snapshot

VEGFR-1 and VEGFR-2: two non-identical twins with a unique physiognomy

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9780470921920.edm139openalex-snapshot

QSAR and Molecular Modeling Approaches for Prediction of Drug Metabolism

inferred← citeshttps://doi.org/10.1002/9783527674381.ch4openalex-snapshot

Discovery Technologies for Drug Repurposing

inferred← citeshttps://doi.org/10.1002/minf.201200126openalex-snapshot

Integrated One‐Against‐One Classifiers as Tools for Virtual Screening of Compound Databases: A Case Study with CNS Inhibitors

inferred← citeshttps://doi.org/10.1002/minf.201600013openalex-snapshot

Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction

inferred← citeshttps://doi.org/10.1002/wcms.1128openalex-snapshot

Shape‐based similarity searching in chemical databases

inferred← citeshttps://doi.org/10.1002/wcms.1152openalex-snapshot

Chemoinformatics applications of cluster analysis

inferred← citeshttps://doi.org/10.1016/j.bmc.2012.03.017openalex-snapshot

Cluster analysis of the DrugBank chemical space using molecular quantum numbers

inferred← citeshttps://doi.org/10.1016/j.drudis.2012.11.008openalex-snapshot

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

inferred← citeshttps://doi.org/10.1016/j.jmgm.2012.06.010openalex-snapshot

Impact of the CXCR4 structure on docking-based virtual screening of HIV entry inhibitors

inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.01.003openalex-snapshot

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00120openalex-snapshot

GESSE: Predicting Drug Side Effects from Drug–Target Relationships

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00134openalex-snapshot

VS-APPLE: A Virtual Screening Algorithm Using Promiscuous Protein–Ligand Complexes

inferred← citeshttps://doi.org/10.1021/ci200542mopenalex-snapshot

Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms

inferred← citeshttps://doi.org/10.1021/ci200562popenalex-snapshot

Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors

inferred← citeshttps://doi.org/10.1021/ci3002638openalex-snapshot

Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations

inferred← citeshttps://doi.org/10.1021/ci400037yopenalex-snapshot

Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance

inferred← citeshttps://doi.org/10.1021/ci400429gopenalex-snapshot

An Integrated Virtual Screening Approach for VEGFR-2 Inhibitors

inferred← citeshttps://doi.org/10.1021/ci400453nopenalex-snapshot

ALFA: Automatic Ligand Flexibility Assignment

inferred← citeshttps://doi.org/10.1021/ci500232gopenalex-snapshot

Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17

inferred← citeshttps://doi.org/10.1080/07391102.2017.1417161openalex-snapshot

On the relationship of anthranilic derivatives structure and the FXR (Farnesoid X receptor) agonist activity

inferred← citeshttps://doi.org/10.1080/08927022.2014.898845openalex-snapshot

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inferred← citeshttps://doi.org/10.1080/1206212x.2019.1703337openalex-snapshot

Network node grouping algorithm and evaluation model based on clustering and Bayesian classifier

inferred← citeshttps://doi.org/10.1109/tla.2016.7459629openalex-snapshot

Gaussian Mixture Models Implementation to Enhance Spectral Clustering

inferred← citeshttps://doi.org/10.1111/cbdd.13416openalex-snapshot

Targeting the Plasmodium falciparum plasmepsin V by ligand‐based virtual screening

inferred← citeshttps://doi.org/10.1111/febs.12268openalex-snapshot

Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it

inferred← citeshttps://doi.org/10.1186/s13321-014-0051-5openalex-snapshot

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

inferred← citeshttps://doi.org/10.1517/17460441.2011.632406openalex-snapshot

Identifying and characterizing promiscuous targets: Implications for virtual screening

inferred← citeshttps://doi.org/10.1517/17460441.2015.1082543openalex-snapshot

Using quantitative systems pharmacology for novel drug discovery

inferred← citeshttps://doi.org/10.2142/biophysico.13.0_149openalex-snapshot

Importance of consensus region of multiple-ligand templates in a virtual screening method

inferred← citeshttps://doi.org/10.2174/0115680266359804251111113649openalex-snapshot

A Novel Perspective on Using Artificial Intelligence and Nanoinformatics to Develop Nanomedicines

inferred← citeshttps://doi.org/10.2174/1389200215666140908102530openalex-snapshot

In silico Prediction of Drug Metabolism by P450

inferred← citeshttps://doi.org/10.2174/15680266113139990028openalex-snapshot

Recent Trends and Future Prospects in Computational GPCR Drug Discovery: From Virtual Screening to Polypharmacology

inferred← citeshttps://doi.org/10.2174/2210289201102010113openalex-snapshot

Predicting Drug Promiscuity Using Spherical Harmonic Surface Shape-Based Similarity Comparisons

inferred← citeshttps://doi.org/10.26434/chemrxiv-2024-dkvf8openalex-snapshot

3D-Pharma, A Ligand-based Virtual Screening toolusing 3D Pharmacophore Fingerprints

inferred← citeshttps://doi.org/10.3389/fchem.2018.00315openalex-snapshot

Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery

inferred← citeshttps://doi.org/10.3389/fchem.2020.00726openalex-snapshot

Computational Approaches in Preclinical Studies on Drug Discovery and Development

inferred← citeshttps://doi.org/10.3390/molecules190710150openalex-snapshot

Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design

inferred← citeshttps://doi.org/10.3390/molecules24142529openalex-snapshot

High Impact: The Role of Promiscuous Binding Sites in Polypharmacology

inferred← citeshttps://doi.org/10.5772/35874openalex-snapshot

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