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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

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Development of a New Scoring Function for Virtual Screening: APBScore.

Jingxiao Bao¹, Xiao He^1,2, John Z H Zhang^1,2,3,4

¹Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.

Journal of Chemical Information and Modeling

|October 14, 2020

Summary

This summary is machine-generated.

We developed Atom Pair-Based Scoring function (APBScore), a new scoring function for molecular docking. APBScore excels in scoring, ranking, and docking, especially for zinc/ligand interactions, and detects atomic collisions.

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Accurate scoring functions are crucial for molecular docking in drug discovery.
Existing scoring functions may struggle with specific interactions like those involving zinc.

Purpose of the Study:

To develop a novel, physics-based scoring function for molecular docking.
To evaluate the performance of the new scoring function against established methods.

Main Methods:

Developed the Atom Pair-Based Scoring function (APBScore).
Incorporated pairwise van der Waals (VDW), electrostatic, and hydrogen bond energies.
Optimized atom-pair VDW interactions and zinc/ligand interactions.
Performed structural minimization and tested on benchmark datasets.

Main Results:

APBScore demonstrated excellent scoring performance compared to traditional functions.
Achieved top-ranking performance for scoring zinc/ligand interactions.
Showed good performance in ranking and docking tasks.
Effectively identified decoy structures with atomic collisions due to VDW optimization.

Conclusions:

APBScore is a simple yet powerful scoring function for molecular docking.
Its accuracy in scoring, ranking, and docking, particularly for metallo-complexes, makes it a valuable tool.
The function's sensitivity to atomic collisions enhances its reliability.