scholarly journals Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

2021 ◽  
Author(s):  
Lorenzo Casbarra ◽  
Piero Procacci
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Drug Discovery ◽  
Binding Free Energy ◽  
Cost Ratio ◽  
Benefit Cost Ratio ◽  
Docking Program ◽  
Benefit Cost ◽  
Overall Reliability ◽  
Absolute Binding Free Energy

AbstractWe 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 instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

2006 ◽  
Vol 125 (8) ◽  
pp. 084901 ◽  
Author(s):  
Guha Jayachandran ◽  
Michael R. Shirts ◽  
Sanghyun Park ◽  
Vijay S. Pande
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Free Energy ◽  
Absolute Binding Free Energy

Extracting atomic contributions to binding free energy from molecular dynamics simulations with mixed solvents (MDmix)

2021 ◽  
Vol 19 ◽  
Author(s):  
Daniel Alvarez- Garcia ◽  
Peter Schmidtke ◽  
Elena Cubero ◽  
Xavier Barril
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Drug Discovery ◽  
Drug Design ◽  
Binding Free Energy ◽  
Mixed Solvents ◽  
Md Simulations ◽  
Molecular Binding ◽  
Dynamics Simulations ◽  
Energy Maps

Background: Mixed solvents MD simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery Method: Mixed solvents MD simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery Result: As such, they are hardly transferable to different molecules. Conclusion: To achieve transferable energies, we present here a method for decomposing the molecular binding free energy into accurate atomic contributions and we demonstrate with two qualitative visual examples how the corrected energy maps better match known binding hotspots and how they can reveal hidden hotspots with actual drug design potential.

Comparative Effectiveness Of Seed Treating And Foliar Insecticides Against Sucking Pests Of Cotton And Impact On Their Natural Enemies

2013 ◽  
Vol 38 (1) ◽  
pp. 61-70 ◽  
Author(s):  
SMA Hossain ◽  
MA Baque ◽  
MR Amin
Keyword(s):  
Natural Enemies ◽  
Untreated Control ◽  
Seed Treatment ◽  
Foliar Spray ◽  
Cost Ratio ◽  
Research Station ◽  
Benefit Cost Ratio ◽  
Benefit Cost ◽  
Thrips Population ◽  
Cotton Cultivar

The Imidacloprid insecticide, Gaucho 70 WS at 1.5, 2.5, 3.5, 4.5 and 5.5 g/kg seed was used as seed treatment and monocrotophos 40 WSC at 1120 ml/ha was applied as foliar spray on CB9 cotton cultivar to suppress aphid, whitefly and thrips, and impact on their natural enemies during 2008-2011 at the Regional Cotton Research Station, Dinajpur, Bangladesh. The activity of natural enemies, such as ladybird beetle, lacewing, syrphid, and spider population on the sucking pests attacking cotton cultivar CB9 and yield of cotton were recorded. Imidacloprid significantly reduced aphid, whitefly, and thrips population on cotton crops compared to untreated control or foliar spray of monocrotophos 40 WSC at 1120 ml/ha. Ladybird beetles, lacewings, syrphids, and spiders were abundant in the field but their population decreased in the treated plots compared to untreated control. The CB9 cotton cultivar produced significantly higher yield (1.73 t/ha) with a benefit cost ratio 12.47 when seeds were treated with Imidacloprid at 5.5 g/kg fuzzy seed. This study indicated that Imidacloprid (Gaucho 70 WS) used as a seed treatment may be suggested to the cotton growers for controlling sucking pests. Bangladesh J. Agril. Res. 38(1): 61-70, March 2013 DOI: http://dx.doi.org/10.3329/bjar.v38i1.15190

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