A quantum-based similarity method in virtual screening
TL;DR: Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.
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Abstract: One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.
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References
•Book
Atoms in molecules : a quantum theory
Richard F. W. Bader
- 01 Jan 1990
TL;DR: In this article, the quantum atom and the topology of the charge desnity of a quantum atom are discussed, as well as the mechanics of an atom in a molecule.
13.8K
Atoms in Molecules
R. F. W. Bader
- 13 Dec 1990
TL;DR: The molecular structure hypothesis is a theory that molecules are collections of atoms linked by bonds. It is not directly related to the physics that governs the motions of the nuclei and electrons that make up the atoms and the bonds. This book aims to develop a theory to underpin the molecular structure hypothesis.
10.5K
Chemical Similarity Searching
TL;DR: The concept of similarity searching is introduced, differentiating it from the more common substructure searching, and the current generation of fragment-based measures that are used for searching chemical structure databases are discussed.
Quantum-Chemical Descriptors in QSAR/QSPR Studies
TL;DR: Applications of quantum chemical descriptors in the development of QSAR/QSPR dealing with the chemical, physical, biochemical, and pharmacological properties of compounds are reviewed.
1.4K