Pose Prediction for Mobile Ground Robots in Uneven Terrain Based on Difference of Heightmaps

Autonomous vehicles can obtain real-time road information using 3D sensors. With road information, vehicles avoid obstacles through real-time path planning to improve their safety and stability. However, most of the research on driverless vehicles have been carried out on urban even driveways, with little consideration of uneven terrain. For an autonomous full tracked vehicle (FTV), the uneven terrain has a great impact on the stability and safety. In this paper, we proposed a method to predict the pose of the FTV based on accurate road elevation information obtained by 3D sensors. If we could predict the pose of the FTV traveling on uneven terrain, we would not only control the active suspension system but also change the driving trajectory to improve the safety and stability. In the first, 3D laser scanners were used to get real-time cloud data points of the terrain for extracting the elevation information of the terrain. Inertial measurement units (IMUs) and GPS are essential to get accurate attitude angle and position information. Then, the dynamics model of the FTV was established to calculate the vehicle’s pose. Finally, the Kalman filter was used to improve the accuracy of the predicted pose. Compared to the traditional method of driverless vehicles, the proposed approach was more suitable for autonomous FTV. The real-world experimental result demonstrated the accuracy and effectiveness of our approach.

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

10.26434/chemrxiv.11733393 ◽

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.

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D3R Grand Challenge 4: Ligand Similarity and MM-GBSA-Based Pose Prediction and Affinity Ranking for BACE-1 Inhibitors

10.26434/chemrxiv.8259074.v1 ◽

2019 ◽

Author(s):

Sukanya Sasmal ◽

Léa El Khoury ◽

David Mobley

Keyword(s):

Binding Mode ◽

Energy Estimates ◽

Poor Correlation ◽

Grand Challenge ◽

Pose Prediction ◽

Design Data ◽

Data Resource ◽

Affinity Ranking ◽

Ligand Similarity ◽

Bace 1

The Drug Design Data Resource (D3R) Grand Challenges present an opportunity to assess, in the context of a blind predictive challenge, the accuracy and the limits of tools and methodologies designed to help guide pharmaceutical drug discovery projects. Here, we report the results of our participation in the D3R Grand Challenge 4, which focused on predicting the binding poses and affinity ranking for compounds targeting the beta-amyloid precursor protein (BACE-1). Our ligand similarity-based protocol using HYBRID (OpenEye Scientific Software) successfully identified poses close to the native binding mode for most of the ligands with less than 2 A RMSD accuracy. Furthermore, we compared the performance of our HYBRID-based approach to that of AutoDock Vina and Dock 6 and found that HYBRID performed better here for pose prediction. We also conducted end-point free energy estimates on protein-ligand complexes using molecular mechanics combined with generalized Born surface area method (MM-GBSA). We found that the binding affinity ranking based on MM-GBSA scores have poor correlation with the experimental values. Finally, the main lessons from our participation in D3R Grand Challenge 4 suggest that: i) the generation of the macrocycles conformers is a key step for successful pose prediction, ii) the protonation states of the BACE-1 binding site should be treated carefully, iii) the MM-GBSA method could not discriminate well between different predicted binding poses, and iv) the MM-GBSA method does not perform well at predicting protein-ligand binding affinities here.

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