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Novel Inhibitor Discovery through Virtual Screening against Multiple Protein Conformations Generated via Ligand-Directed Modeling: A Maternal Embryonic Leucine Zipper Kinase Example

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Comparative Protein Structure Modeling Using MODELLER

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The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme

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Maternal embryonic leucine zipper kinase transcript abundance correlates with malignancy grade in human astrocytomas

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Challenges and advances in computational docking: 2009 in review

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Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells

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In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking

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

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Improving database enrichment through ensemble docking

inferredcites →https://doi.org/10.1016/j.bmc.2008.10.041openalex-snapshot

The importance of CH/π hydrogen bonds in rational drug design: An ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase

inferredcites →https://doi.org/10.1016/j.drudis.2009.01.003openalex-snapshot

Managing protein flexibility in docking and its applications

inferredcites →https://doi.org/10.1016/j.drudis.2010.10.003openalex-snapshot

PubChem as a public resource for drug discovery

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Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

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Capturing Structure−Activity Relationships from Chemogenomic Spaces

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Understanding the Impact of the P-loop Conformation on Kinase Selectivity

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Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures

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Utilizing Experimental Data for Reducing Ensemble Size in Flexible-Protein Docking

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

inferredcites →https://doi.org/10.1021/ci800081sopenalex-snapshot

Fully Automated Molecular Mechanics Based Induced Fit Protein−Ligand Docking Method

inferredcites →https://doi.org/10.1021/ci9003706openalex-snapshot

Molecular Docking Screens Using Comparative Models of Proteins

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Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

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Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme

inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot

Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations

inferredcites →https://doi.org/10.1021/jm030209yopenalex-snapshot

Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy

inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

inferredcites →https://doi.org/10.1021/jm049798dopenalex-snapshot

Comparison of Automated Docking Programs as Virtual Screening Tools

inferredcites →https://doi.org/10.1021/jm050040jopenalex-snapshot

Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data

inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot

Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

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

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm101020zopenalex-snapshot

Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications

inferredcites →https://doi.org/10.1021/jm8005977openalex-snapshot

The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery

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Synthesis, Kinase Inhibitory Potencies, and in Vitro Antiproliferative Evaluation of New Pim Kinase Inhibitors

inferredcites →https://doi.org/10.1021/jp911085dopenalex-snapshot

Dynamic Ligand-Induced-Fit Simulation via Enhanced Conformational Samplings and Ensemble Dockings: A Survivin Example

inferredcites →https://doi.org/10.1038/nbt1358openalex-snapshot

A quantitative analysis of kinase inhibitor selectivity

inferredcites →https://doi.org/10.1038/nchembio799openalex-snapshot

Rational design of inhibitors that bind to inactive kinase conformations

inferredcites →https://doi.org/10.1038/nrc2559openalex-snapshot

Targeting cancer with small molecule kinase inhibitors

inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot

Implications of protein flexibility for drug discovery

inferredcites →https://doi.org/10.1042/bj20070797openalex-snapshot

The selectivity of protein kinase inhibitors: a further update

inferredcites →https://doi.org/10.1073/pnas.0904214106openalex-snapshot

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

inferredcites →https://doi.org/10.1073/pnas.1104614108openalex-snapshot

Pathway and mechanism of drug binding to G-protein-coupled receptors

inferredcites →https://doi.org/10.1073/pnas.1201940109openalex-snapshot

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

inferredcites →https://doi.org/10.1093/nar/gkp965openalex-snapshot

An overview of the PubChem BioAssay resource

inferredcites →https://doi.org/10.1158/0008-5472.can-04-4531openalex-snapshot

Maternal Embryonic Leucine Zipper Kinase/Murine Protein Serine-Threonine Kinase 38 Is a Promising Therapeutic Target for Multiple Cancers

inferredcites →https://doi.org/10.1186/bcr1650openalex-snapshot

Involvement of maternal embryonic leucine zipper kinase (MELK) in mammary carcinogenesis through interaction with Bcl-G, a pro-apoptotic member of the Bcl-2 family

inferredcites →https://doi.org/10.1517/17460441.2010.524924openalex-snapshot

Exploiting PubChem for virtual screening

inferredcites →https://doi.org/10.4161/cc.8.5.7879openalex-snapshot

Benzo[e]pyridoindoles, novel inhibitors of the Aurora kinases

What points at this work

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

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Consensus Virtual Screening Identified [1,2,4]Triazolo[1,5‐b]isoquinolines As MELK Inhibitor Chemotypes

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Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures

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Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries

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Docking Screens for Novel Ligands Conferring New Biology

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Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations

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Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity

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Fragment-Based Discovery of Type I Inhibitors of Maternal Embryonic Leucine Zipper Kinase

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Comparative inhibitory profile and distribution of bacterial PARPs, using Clostridioides difficile CD160 PARP as a model

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In-silico identification of inhibitors against mutated BCR-ABL protein of chronic myeloid leukemia: a virtual screening and molecular dynamics simulation study

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Getting the most out of PubChem for virtual screening

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Considerations of Protein Subpockets in Fragment‐Based Drug Design

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Ligand Pose and Orientational Sampling in Molecular Docking

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Multi-Kinase Inhibitor C1 Triggers Mitotic Catastrophe of Glioma Stem Cells Mainly through MELK Kinase Inhibition

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The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set

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OTSSP167 Abrogates Mitotic Checkpoint through Inhibiting Multiple Mitotic Kinases

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A Novel Tetramethylpyrazine Chalcone Hybrid- HCTMPPK, as a Potential Anti-Lung Cancer Agent by Downregulating MELK

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Spatiotemporal regulation of MELK during mitosis

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

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MUC21 induces the viability and migration of glioblastoma via the STAT3/AKT pathway

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Docking Methodologies and Recent Advances

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Docking Methodologies and Recent Advances

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Sclerostin small-molecule inhibitors promote osteogenesis by activating canonical Wnt and BMP pathways

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