Structure‐based study to identify alkaloids as promising cytochrome P450 (CYP1A1) inhibitors: An in silico approach using virtual screening, molecular dynamic simulations, and binding free energy calculation
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DOI: 10.1002/jcb.30302
Abstract: Carcinogens present in smokeless tobacco (SLT) like tobacco‐specific nitrosamines can be metabolized by the cytochrome P450 (CYP450) enzyme. Functionally, the CYP450 enzyme resides in a heme pigment to perform the catalytic activity. The CYP1A1 is… read more here.
Keywords: binding free; virtual screening; free energy; cytochrome p450 ... See more keywords
Effect of sampling on BACE‐1 ligands binding free energy predictions via MM‐PBSA calculations
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DOI: 10.1002/jcc.24839
Abstract: The BACE‐1 enzyme is a prime target to find a cure to Alzheimer's disease. In this article, we used the MM‐PBSA approach to compute the binding free energies of 46 reported ligands to this enzyme.… read more here.
Keywords: bace; effect sampling; bace ligands; sampling bace ... See more keywords
Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors
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DOI: 10.1002/jcc.26036
Abstract: Alchemical Grid Dock (AlGDock) is open‐source software designed to compute the binding potential of mean force—the binding free energy between a flexible ligand and a rigid receptor—for a small organic ligand and a biological macromolecule.… read more here.
Keywords: dock algdock; alchemical grid; algdock; grid dock ... See more keywords
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses
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DOI: 10.1002/jcc.26078
Abstract: We propose a free energy calculation method for receptor–ligand binding, which have multiple binding poses that avoids exhaustive enumeration of the poses. For systems with multiple binding poses, the standard procedure is to enumerate orientations… read more here.
Keywords: binding poses; energy; calculation; binding free ... See more keywords
Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-018-0158-2
Abstract: We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim… read more here.
Keywords: challenge; free energies; binding free; host guest ... See more keywords
A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase–ligand and FKBP–ligand systems
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-020-00302-4
Abstract: In this study, a new method is proposed for calculating the relative binding free energy between a ligand and a protein, derived from a free energy variational principle (FEVP). To address the shortcomings of the… read more here.
Keywords: pim kinase; energy; binding free; ligand ... See more keywords
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-021-00385-7
Abstract: In this study, we report binding free energy calculations of various drugs-of-abuse to Cucurbit-[8]-uril as part of the SAMPL8 blind challenge. Force-field parameters were obtained from force-matching with different quantum mechanical levels of theory. The… read more here.
Keywords: usepackage; free energies; binding free; host ... See more keywords
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-021-00388-4
Abstract: We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many… read more here.
Keywords: guest systems; binding free; sampl6 sampl7; host guest ... See more keywords
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge
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DOI: 10.1007/s10822-021-00437-y
Abstract: We report the results of our participation in the SAMPL8 GDCC Blind Challenge for host-guest binding affinity predictions. Absolute binding affinity prediction is of central importance to the biophysics of molecular association and pharmaceutical discovery.… read more here.
Keywords: binding free; free energy; host guest; force ... See more keywords
Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation
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DOI: 10.1007/s11030-020-10135-w
Abstract: Abstract The pandemic outbreak of the Corona viral infection has become a critical global health issue. Biophysical and structural evidence shows that spike protein possesses a high binding affinity towards host angiotensin-converting enzyme 2 and… read more here.
Keywords: potential inhibitors; energy; molecular dynamics; binding free ... See more keywords
Discovery and design of new PI3K inhibitors through pharmacophore-based virtual screening, molecular docking, and binding free energy analysis
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DOI: 10.1007/s11224-018-1154-9
Abstract: Phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/the mammalian target of rapamycin (mTOR) signaling pathway is one of the sought after therapeutic target for treating human cancers. This pathway is often hyper activated in cancers. In the… read more here.
Keywords: pi3k; energy; screening; binding free ... See more keywords