Molecular Similarity: Methods and Performance
Chaoqian Cai
School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Search for more papers by this authorJiayu Gong
School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Search for more papers by this authorXiaofeng Liu
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Search for more papers by this authorCorresponding Author
Daqi Gao
School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
Daqi Gao, School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
Honglin Li, State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Tel.: 0086-021-64250213; Fax: 0086-021-64250213
Search for more papers by this authorCorresponding Author
Honglin Li
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Daqi Gao, School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
Honglin Li, State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Tel.: 0086-021-64250213; Fax: 0086-021-64250213
Search for more papers by this authorChaoqian Cai
School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Search for more papers by this authorJiayu Gong
School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Search for more papers by this authorXiaofeng Liu
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Search for more papers by this authorCorresponding Author
Daqi Gao
School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
Daqi Gao, School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
Honglin Li, State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Tel.: 0086-021-64250213; Fax: 0086-021-64250213
Search for more papers by this authorCorresponding Author
Honglin Li
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Daqi Gao, School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
Honglin Li, State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Tel.: 0086-021-64250213; Fax: 0086-021-64250213
Search for more papers by this authorAbstract
Molecular similarity has long been a hot topic, which has been evaluated and compared by various approaches and plays a significant role in protein-ligand and protein-protein interactions recognition. There are currently many types of molecular similarity evaluation methods with their own advantages and disadvantages. Molecular fingerprints are the most common methods for molecular similarity evaluation which only concern about rapid 2D common substructure retrieval but lack the ability to encode the information about 3D conformers. 3D molecular descriptor based methods bear the advantages of representing the structure information of a conformer, but the descriptors are not guaranteed to describe the molecules precisely. Molecular alignment based methods try to superimpose two molecules and evaluate the similarity using the optimal poses which are generally more precise than the molecular descriptor but require a time-consuming optimization process. Pharmacophore based methods only focus on the chemical features about a molecule and are not capable of dealing with the molecular shape similarity. In order to evaluate the performance of molecular similarity based screening, many kinds of metrics are available, e.g., visual representation, quantitative measurements and scaffold hopping ability measurements. Further applications of molecular similarity include construction of molecule interaction network or generation of diverse compounds library.
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