scholarly journals Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand–Protein Complexes: A Brute Force Approach That Is Fast and Accurate

2015 ◽  
Vol 11 (4) ◽  
pp. 1928-1938 ◽  
Author(s):  
Liao Y. Chen
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Protein Complexes ◽  
Binding Free Energy ◽  
Steered Molecular Dynamics ◽  
Brute Force ◽  
Brute Force Approach ◽  
Absolute Binding Free Energy

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

Assessing the ligand selectivity of sphingosine kinases using molecular dynamics and MM-PBSA binding free energy calculations

2016 ◽  
Vol 12 (4) ◽  
pp. 1174-1182 ◽  
Author(s):  
Liang Fang ◽  
Xiaojian Wang ◽  
Meiyang Xi ◽  
Tianqi Liu ◽  
Dali Yin
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Model Building ◽  
Binding Free Energy ◽  
Homology Model ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Ligand Selectivity ◽  
Sphingosine Kinases ◽  
Binding Free Energy Calculations

Three residues of SK1 were identified important for selective SK1 inhibitory activity via SK2 homology model building, molecular dynamics simulation, and MM-PBSA studies.

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