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Protein Kinases: Docking and Homology Modeling Reliability

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What this work says

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

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

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Gaussian docking functions

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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Improved protein–ligand docking using GOLD

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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

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MUSTANG: A multiple structural alignment algorithm

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Erlotinib: Small-molecule targeted therapy in the treatmentof non-small-cell lung cancer

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Assessing the performance of OMEGA with respect to retrieving bioactive conformations

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Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy

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Protein−Ligand Docking against Non-Native Protein Conformers

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QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors

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An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

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

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A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction

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Soft Docking and Multiple Receptor Conformations in Virtual Screening

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DoMCoSAR: A Novel Approach for Establishing the Docking Mode That Is Consistent with the Structure−Activity Relationship. Application to HIV-1 Protease Inhibitors and VEGF Receptor Tyrosine Kinase Inhibitors

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Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug

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Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2

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The specificities of protein kinase inhibitors: an update

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Structure and Regulation of the Human Nek2 Centrosomal Kinase

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

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ExPASy: the proteomics server for in-depth protein knowledge and analysis

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Modeling of loops in protein structures

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Functional diversity of human protein kinase splice variants marks significant expansion of human kinome

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ZD1839 (IRESSA™): a selective EGFR-TK inhibitor

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Structure Selection for Protein Kinase Docking and Virtual Screening:Homology Models or Crystal Structures?

What points at this work

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

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A pose prediction approach based on ligand 3D shape similarity

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D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

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D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

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Protein Structure Prediction and Homology Modeling

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Protein structure prediction

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Assessing protein kinase target similarity: Comparing sequence, structure, and cheminformatics approaches

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POSIT: Flexible Shape-Guided Docking For Pose Prediction

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Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization

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Use of BODIPY-Labeled ATP Analogues in the Development and Validation of a Fluorescence Polarization-Based Assay for Screening of Kinase Inhibitors

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Potential and Limitations of Ensemble Docking

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Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome

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Identification of New Fyn Kinase Inhibitors Using a FLAP-Based Approach

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The Application of Statistical Methods to Cognate Docking: A Path Forward?

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Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening

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Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA

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Extensive Consensus Docking Evaluation for Ligand Pose Prediction and Virtual Screening Studies

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