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
Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-017-0054-1
Abstract: Our participation to the D3R Grand Challenge 2 involved a protocol in two steps, with an initial analysis of the available structural data from the PDB allowing the selection of the most appropriate combination of… read more here.
Keywords: blinded evaluation; energy calculations; evaluation farnesoid; free energy ... See more keywords
Structural, electronic and magnetic properties of the MnGa(111)-1 × 2 and 2 × 2 reconstructions: Spin polarized first principles total energy calculations
Sign Up to like & getrecommendations! Published in 2017 at "Applied Surface Science"
DOI: 10.1016/j.apsusc.2017.04.241
Abstract: Abstract Using first principles total energy calculations within the periodic spin polarized density functional theory, we have investigated the structural, electronic, and magnetic properties of manganese gallium (MnGa) alloys. Specifically, we explore the MnGa(111)-1 × 2 and… read more here.
Keywords: energy; energy calculations; magnetic properties; principles total ... See more keywords
Free energy calculations for adsorption-induced deformation of flexible metal–organic frameworks
Sign Up to like & getrecommendations! Published in 2019 at "Current Opinion in Chemical Engineering"
DOI: 10.1016/j.coche.2019.01.001
Abstract: Flexible metal–organic frameworks (MOFs) are characterized by their responsiveness to guest adsorption, which is called ‘gate opening’ or ‘breathing’. Free energy calculations are tools for evaluating the stability of these systems, and are crucial for… read more here.
Keywords: adsorption; metal organic; flexible metal; free energy ... See more keywords
Targeting protein tyrosine phosphatase to unravel possible inhibitors for Streptococcus pneumoniae using molecular docking, molecular dynamics simulations coupled with free energy calculations.
Sign Up to like & getrecommendations! Published in 2020 at "Life sciences"
DOI: 10.1016/j.lfs.2020.118621
Abstract: AIMS Protein tyrosine phosphatase (PTP-CPS4B) is a signaling enzyme that is essential for a wide range of cellular processes, like metabolism, proliferation, survival and motility. Studies suggest that PTPs are vital for the production of… read more here.
Keywords: energy calculations; ptp cps4b; cps4b; free energy ... See more keywords
Free energy calculations of RNA interactions.
Sign Up to like & getrecommendations! Published in 2019 at "Methods"
DOI: 10.1016/j.ymeth.2019.02.014
Abstract: This review discusses the use of molecular dynamics free energy calculations for characterizing RNA interactions, with particular emphasis on molecular recognition events involved in mRNA translation on the ribosome. The general methodology for efficient free… read more here.
Keywords: methodology; energy calculations; energy; rna interactions ... See more keywords
Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c00132
Abstract: A tremendous research and development effort was exerted toward combating chronic hepatitis C, ultimately leading to curative oral treatments, all of which are targeting viral proteins. Despite the advantage of numerous targets allowing for broad… read more here.
Keywords: calculations prioritization; energy calculations; energy; evaluation free ... See more keywords
An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c00520
Abstract: Alchemical free energy calculations typically rely on intermediate states to bridge between the relevant phase spaces of the two end states. These intermediate states are usually created by mixing the energies or parameters of the… read more here.
Keywords: intermediate states; energy calculations; energy; conventional intermediate ... See more keywords
Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c00834
Abstract: Covalent inhibitors have been gaining increased attention in drug discovery due to their beneficial properties such as long residence time, high biochemical efficiency, and specificity. Optimization of covalent inhibitors is a complex task that involves… read more here.
Keywords: selectivity; covalent inhibitors; free energy; energy calculations ... See more keywords
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations
Sign Up to like & getrecommendations! Published in 2021 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c01424
Abstract: Relative free energy calculations are fast becoming a critical part of early stage pharmaceutical design, making it important to know how to obtain the best performance with these calculations in applications that could span hundreds… read more here.
Keywords: relative binding; energy calculations; binding free; performance ... See more keywords
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.2c00348
Abstract: Here, we show that alchemical free energy calculations can quantitatively compute the effect of mutations at the protein–protein interface. As a test case, we have used the protein complex formed by the small Rho-GTPase CDC42… read more here.
Keywords: pak1; alchemical free; energy calculations; free energy ... See more keywords