GalaxyDock2: Protein-ligand docking using beta-complex and global optimization

2013 ◽  
Vol 34 (30) ◽  
pp. 2647-2656 ◽  
Author(s):  
Woong-Hee Shin ◽  
Jae-Kwan Kim ◽  
Deok-Soo Kim ◽  
Chaok Seok
Keyword(s):  
Global Optimization ◽  
Ligand Docking

Global Optimization

1993 ◽  
Author(s):  
Reiner Horst ◽  
Hoang Tuy
Keyword(s):  
Global Optimization

Probability Models in Global Optimization

Informatica ◽  
2016 ◽  
Vol 27 (2) ◽  
pp. 323-334 ◽  
Author(s):  
James M. Calvin
Keyword(s):  
Global Optimization ◽  
Probability Models

Evaluation of Grey Wolf Optimization Algorithm on Rigid and Flexible Receptor Docking

2020 ◽  
Author(s):  
Kin Meng Wong ◽  
Shirley Siu
Keyword(s):  
Scoring Function ◽  
Ligand Docking ◽  
Receptor Protein ◽  
Pose Prediction ◽  
Grey Wolf ◽  
Success Rates ◽  
Autodock Vina ◽  
Grey Wolf Optimization ◽  
Structure Based Drug Design ◽  
Docking Program

Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein in current structure-based drug design. In this paper, we evaluate the performance of grey wolf optimization (GWO) in protein-ligand docking. Two versions of the GWO docking program – the original GWO and the modified one with random walk – were implemented based on AutoDock Vina. Our rigid docking experiments show that the GWO programs have enhanced exploration capability leading to significant speedup in the search while maintaining comparable binding pose prediction accuracy to AutoDock Vina. For flexible receptor docking, the GWO methods are competitive in pose ranking but lower in success rates than AutoDockFR. Successful redocking of all the flexible cases to their holo structures reveals that inaccurate scoring function and lack of proper treatment of backbone are the major causes of docking failures.

Hybrid orthogonal CMAES for solving global optimization problems

2013 ◽  
Vol 32 (4) ◽  
pp. 981-985
Author(s):  
Ya-fei HUANG ◽  
Xi-ming LIANG ◽  
Yi-xiong CHEN
Keyword(s):  
Global Optimization ◽  
Optimization Problems
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