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Active Site Pressurization: A New Tool for Structure-Guided Drug Design and Other Studies of Protein Flexibility

https://doi.org/10.1021/ci7004725
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What this work says

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

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How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
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Development and testing of a general amber force field
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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
inferredcites →https://doi.org/10.1002/prot.10400openalex-snapshot
Molecular dynamics simulations of a helicase
inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot
Protein–ligand docking: Current status and future challenges
inferredcites →https://doi.org/10.1006/jmbi.2000.4154openalex-snapshot
How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1006/jmbi.2000.4155openalex-snapshot
How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1016/0167-7322(88)80022-9openalex-snapshot
Computer Simulation of Liquids
inferredcites →https://doi.org/10.1016/j.jinorgbio.2004.02.007openalex-snapshot
A survey of active site access channels in cytochromes P450
inferredcites →https://doi.org/10.1016/j.jmb.2003.08.031openalex-snapshot
Structural Characterization of the GSK-3β Active Site Using Selective and Non-selective ATP-mimetic Inhibitors
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Crystal Structures of Complexes of PcrA DNA Helicase with a DNA Substrate Indicate an Inchworm Mechanism
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Crystal Structure of Glycogen Synthase Kinase 3β
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Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case
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Structure of GSK3beta reveals a primed phosphorylation mechanism.
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Untangling tau hyperphosphorylation in drug design for neurodegenerative diseases
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Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?
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Modelling protein unfolding: a solvent insertion protocol
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Phase diagrams of Lennard-Jones fluids
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Detection, delineation, measurement and display of cavities in macromolecular structures
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POSSIBLE PATHWAY(S) OF TESTOSTERONE EGRESS FROM THE ACTIVE SITE OF CYTOCHROME P450 2B1: A STEERED MOLECULAR DYNAMICS SIMULATION
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Possible Pathway(s) of Metyrapone Egress from the Active Site of Cytochrome P450 3A4: A Molecular Dynamics Simulation
inferredcites →https://doi.org/10.1529/biophysj.106.088203openalex-snapshot
Structure-Based Model of the Stepping Motor of PcrA Helicase

What points at this work

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

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Protein Flexibility in Structure‐Based Virtual Screening: From Models to Algorithms
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Using Ligand‐Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo‐Like Kinase 1
inferred← citeshttps://doi.org/10.1002/anie.201205676openalex-snapshot
Using Ligand‐Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo‐Like Kinase 1
inferred← citeshttps://doi.org/10.1002/chin.200843220openalex-snapshot
ChemInform Abstract: Active Site Pressurization: A New Tool for Structure‐Guided Drug Design and Other Studies of Protein Flexibility.
inferred← citeshttps://doi.org/10.1002/minf.200900078openalex-snapshot
In Pursuit of Fully Flexible Protein‐Ligand Docking: Modeling the Bilateral Mechanism of Binding
inferred← citeshttps://doi.org/10.1002/qsar.200810177openalex-snapshot
A Study of CDK2 Inhibitors Using a Novel 3D‐QSAR Method Exploiting Receptor Flexibility
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inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_13openalex-snapshot
Molecular Modeling of Tau Proline-Directed Protein Kinase (PDPK) Inhibitors
inferred← citeshttps://doi.org/10.1007/s00894-013-2008-4openalex-snapshot
The study of interactions between DNA and PcrA DNA helicase by using targeted molecular dynamic simulations
inferred← citeshttps://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot
Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
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Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins
inferred← citeshttps://doi.org/10.1016/s0065-7743(09)04401-7openalex-snapshot
Chapter 1 Recent Advances in the Discovery of GSK-3 Inhibitors and a Perspective on their Utility for the Treatment of Alzheimer's Disease
inferred← citeshttps://doi.org/10.1021/acs.jpclett.6b01525openalex-snapshot
Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design
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Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics
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Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
inferred← citeshttps://doi.org/10.1080/07391102.2014.909744openalex-snapshot
How good areensemblesin improving QSAR models? The case witheCoRIA
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GPCRs through the keyhole: the role of protein flexibility in ligand binding to β-adrenoceptors
inferred← citeshttps://doi.org/10.2174/157340909789577856openalex-snapshot
Modeling Reality for Optimal Docking of Small Molecules to Biological Targets
inferred← citeshttps://doi.org/10.22028/d291-22611openalex-snapshot
Computational design and analysis of binding pockets at protein-protein interaction interfaces
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Description and assessment of a model for GSK-3β database virtual screening
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Investigation of the Flexibility of Protein Kinases Implicated in the Pathology of Alzheimer’s Disease
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Overview of Computational Methods Employed in Early-Stage Drug Discovery
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