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 curren...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 finger- prints are the most common methods for molecular similarity evaluation which only concern about rapid 2D com- mon substructure retrieval but lack the ability to encode the information about 3D conformers. 3D molecular de- scriptor based methods bear the advantages of representing the structure information of a conformer, but the de- scriptors are not guaranteed to describe the molecules precisely. Molecular alignment based methods try to super- impose 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 or- der 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 li- brary.展开更多
基金the Fundamental Research Funds for the Central Universities,the National Natural Science Foundation of China，the Special Fund for Major State Basic Research Project，the Shanghai Committee of Science and Technology，the 863 Hi-Tech Program of China (No.2012AA020308).Honglin Li is also sponsored by Program for New Century Excellent Talents in University
文摘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 finger- prints are the most common methods for molecular similarity evaluation which only concern about rapid 2D com- mon substructure retrieval but lack the ability to encode the information about 3D conformers. 3D molecular de- scriptor based methods bear the advantages of representing the structure information of a conformer, but the de- scriptors are not guaranteed to describe the molecules precisely. Molecular alignment based methods try to super- impose 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 or- der 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 li- brary.
