KLK14 interactions with HAI‐1 and HAI‐2 serine protease inhibitors: A molecular dynamics and relative free‐energy calculations study
Sign Up to like & getrecommendations! Published in 2017 at "Cell Biology International"
DOI: 10.1002/cbin.10839
Abstract: Kallikrein 14 (KLK14) is a serine protease linked to several pathologies including prostate cancer and positively correlates with Gleason score. Though KLK14 functioning in cancer is poorly understood, it has been implicated in HGF/Met signaling,… read more here.
Keywords: hai hai; energy calculations; serine protease; hai ... See more keywords
Challenges in Elucidating the Free Energy Scheme of the Laccase Catalyzed Reduction of Oxygen
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DOI: 10.1002/cctc.202200878
Abstract: Artificial redox catalysts are typically limited by unfavorable scaling relations of reaction intermediates leading to a significant overpotential in multi‐electron redox reactions such as for example the oxygen reduction reaction (ORR). The multicopper oxidase laccase… read more here.
Keywords: energy scheme; laccase catalyzed; free energy; laccase ... See more keywords
Spin‐projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B−DNA by Singlet Oxygen
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DOI: 10.1002/cphc.202000978
Abstract: Abstract Guanine is the most susceptible base to oxidation damage induced by reactive oxygen species including singlet oxygen (1O2, 1Δg). We clarify whether the first step of guanine oxidation in B−DNA proceeds via either a… read more here.
Keywords: oxygen; guanine; energy; spin ... See more keywords
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
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Cellular Biochemistry"
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
Estimation of relative free energies of binding using pre‐computed ensembles based on the single‐step free energy perturbation and the site‐identification by Ligand competitive saturation approaches
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24522
Abstract: Accurate and rapid estimation of relative binding affinities of ligand‐protein complexes is a requirement of computational methods for their effective use in rational ligand design. Of the approaches commonly used, free energy perturbation (FEP) methods… read more here.
Keywords: energy; estimation relative; energy perturbation; relative free ... See more keywords
Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25338
Abstract: We have performed hybrid quantum‐classical metadynamics simulations and quantum chemical calculations to investigate the free energy landscapes of intramolecular proton transfer and associated tautomeric equilibrium in pyridoxal 5 ′ ‐phosphate (PLP) Schiff Bases, namely the… read more here.
Keywords: energy landscapes; plp; active site; free energy ... See more keywords
Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25520
Abstract: Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the simulation along prespecified collective variables (CVs),… read more here.
Keywords: enhanced sampling; molecular enhanced; energy; exploration ... See more keywords
Weighted least square analysis method for free energy calculations
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25580
Abstract: Free energy calculation is an efficient way for studying rare event dynamics. For a complex rare event dynamics, multiple reaction coordinates may be required to describe the transition path between equilibrium states. Theoretically, a one‐dimensional… read more here.
Keywords: analysis method; free energy; transition path; energy ... See more keywords
Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computational Chemistry"
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
Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26877
Abstract: We describe the theory of the so‐called common‐core/serial‐atom‐insertion (CC/SAI) approach to compute alchemical free energy differences and its practical implementation in a Python package called Transformato. CC/SAI is not tied to a specific biomolecular simulation… read more here.
Keywords: alchemical free; molecular dynamics; energy; free energy ... See more keywords