scholarly journals Skewed thermodynamic geometry and optimal free energy estimation

2020 ◽  
Vol 153 (24) ◽  
pp. 244119
Author(s):  
Steven Blaber ◽  
David A. Sivak
Keyword(s):  
Free Energy ◽  
Energy Estimation ◽  
Thermodynamic Geometry

Generalized Born implicit solvent models for small molecule hydration free energies

2017 ◽  
Vol 19 (2) ◽  
pp. 1677-1685 ◽  
Author(s):  
Martin Brieg ◽  
Julia Setzler ◽  
Steffen Albert ◽  
Wolfgang Wenzel
Keyword(s):  
Free Energy ◽  
Small Molecules ◽  
Implicit Solvent ◽  
Free Energies ◽  
Hydration Free Energy ◽  
Energy Estimation ◽  
Generalized Born ◽  
Solvent Models ◽  
Molecular Force ◽  
Implicit Solvent Models

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects.

Docking, Binding Free Energy Estimation, and MD Simulation of Newly Designed CQ and HCQ Analogues Against the Spike-ACE2 Complex of SARS-CoV-2

2021 ◽  
Vol 6 (4) ◽  
pp. 77-89
Author(s):  
Anjoomaara H. Patel ◽  
Riya B. Patel ◽  
MahammadHussain J. Memon ◽  
Samiya S. Patel ◽  
Sharav A. Desai ◽  
...  
Keyword(s):  
Free Energy ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Docking Studies ◽  
Radius Of Gyration ◽  
Ligand Interaction ◽  
Energy Estimation ◽  
Efficacious Treatment ◽  
Protein Ligand Interaction ◽  
Derivatives Of

The coronavirus disease 2019 (COVID-19) virus has been spreading rapidly, and scientists are endeavouring to discover drugs for its efficacious treatment. Chloroquine phosphate, an old drug for treatment of malaria, has shown to have apparent efficacy and acceptable safety against COVID-19. As a part of Drug Discovery Hackathon-2020, in this study, the authors have tried making the derivatives of CQ and HCQ using MarvinSketch by ChemAxon. Molecular docking studies of these ligands were performed using Glide by Schrodinger, and ADME profiles were obtained by using QikProp. The obtained results after data analysis demonstrated that ligands HCQ_imidazoll, choloroquine_3c, HCQ_pyrrolC had good binding affinity and complied with all the ADME parameters. The molecular dynamic simulation of these ligands in complex with the 2019-nCoV RBD/ACE-2-B0AT1 complex PDB ID: 6M17 were carried out, and the parameters like RMSD, RMSF, and radius of gyration were observed to understand the fluctuations and protein-ligand interaction.

scholarly journals Targeted free energy estimation via learned mappings

2020 ◽  
Vol 153 (14) ◽  
pp. 144112 ◽  
Author(s):  
Peter Wirnsberger ◽  
Andrew J. Ballard ◽  
George Papamakarios ◽  
Stuart Abercrombie ◽  
Sébastien Racanière ◽  
...  
Keyword(s):  
Free Energy ◽  
Energy Estimation

scholarly journals Theory of binless multi-state free energy estimation with applications to protein-ligand binding

2012 ◽  
Vol 136 (14) ◽  
pp. 144102 ◽  
Author(s):  
Zhiqiang Tan ◽  
Emilio Gallicchio ◽  
Mauro Lapelosa ◽  
Ronald M. Levy
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Energy Estimation

scholarly journals Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation

RNA ◽  
2009 ◽  
Vol 15 (12) ◽  
pp. 2248-2263 ◽  
Author(s):  
J. Zhang ◽  
J. Dundas ◽  
M. Lin ◽  
R. Chen ◽  
W. Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Three Dimensional ◽  
Energy Estimation

scholarly journals A GEOMETRIC APPROACH TO CORRELATIONS AND QUARK NUMBER SUSCEPTIBILITIES

2012 ◽  
Vol 27 (10) ◽  
pp. 1250055 ◽  
Author(s):  
STEFANO BELLUCCI ◽  
VINOD CHANDRA ◽  
BHUPENDRA NATH TIWARI
Keyword(s):  
Free Energy ◽  
Critical Temperature ◽  
Finite Temperature ◽  
Geometric Approach ◽  
Geometric Realization ◽  
Thermal Fluctuations ◽  
Quark Number ◽  
Self Consistent ◽  
Thermodynamic Geometry ◽  
Quark Number Susceptibility

We study the thermodynamic geometry arising from the free energy for the two- and three-flavor finite temperature hot QCD near the critical temperature. We develop a geometric notion for QCD thermodynamics, relating it with the existing microscopic quantities, e.g. quark-number susceptibility, which appears naturally within an approximately self-consistent resummation of perturbative QCD. We further incorporate thermal fluctuations in the free energy, thus yielding the geometric properties of local and global chemical correlations. These investigations are perturbative in nature. Nevertheless, one could apply the same line of thought for the geometric realization of underlying quark susceptibilities, either in the fabric of lattice QCD or in that of nonperturbative QCD.

scholarly journals Drug Repurposing Against SARS-CoV-2 Using E-Pharmacophore Based Virtual Screening and Molecular Docking with Main Protease as the Target

2020 ◽  
Author(s):  
arun kumar ◽  
Sharanya C.S ◽  
Abhithaj J ◽  
Dileep Francis ◽  
Sadasivan C
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Drug Target ◽  
Binding Free Energy ◽  
Drug Repurposing ◽  
Energy Calculation ◽  
Viral Protease ◽  
Energy Estimation ◽  
Main Protease ◽  
Potential Inhibitors

Since its first report in December 2019 from China the COVID-19 pandemic caused by the beta-coronavirus SARS-CoV-2 has spread at an alarming pace infecting about 26 lakh, and claiming the lives of more than 1.8 lakh individuals across the globe. Although social quarantine measures have succeeded in containing the spread of the virus to some extent, the lack of a clinically approved vaccine or drug remains the biggest bottleneck in combating the pandemic. Drug repurposing can expedite the process of drug development by identifying known drugs which are effective against SARS-CoV-2. The SARS-CoV-2 main protease is a promising drug target due to its indispensable role in viral multiplication inside the host. In the present study an E-pharmacophore hypothesis was generated using the crystal structure of the viral protease in complex with an imidazole carbaximide inhibitor as the drug target. Drugs available in the superDRUG2 database were used to identify candidate drugs for repurposing. The hits were further screened using a structure based approach involving molecular docking at different precisions. The most promising drugs were subjected to binding free energy estimation using MM-GBSA. Among the 4600 drugs screened 17 drugs were identified as candidate inhibitors of the viral protease based on the glide scores obtained from molecular docking. Binding free energy calculation showed that six drugs viz, Binifibrate, Macimorelin acetate, Bamifylline, Rilmazafon, Afatinib and Ezetimibe can act as potential inhibitors of the viral protease.

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