PocketShape

The interactions between proteins and other molecules are critical to a lot of biological processes, e.g. cellular signaling, regulation of cell cycles. Due to the fact that the functions of proteins are not necessarily correlated with protein sequence or fold, local feature analysis of proteins especially the pattern of binding sites may be another way to further understand protein functions and structures. In this study, a 3D structure based evaluation method for exploring the binding site similarity named PocketShape is presented. By means of structure-based alignment, PocketShape is capable of detecting common patterns or residue reservation between binding sites which are not required to possess continuous residues or to be homologous. Further possible application of PocketShape includes: prediction of a drug candidate’s off-target interactions, prediction of new target for known drugs, prediction of a protein’s function, protein classification. A protein profiling test carried out on protein kinase dataset demonstrates that PocketShape is capable of retrieving binding sites with common pattern.

User Login


Contact us


Honglin Li's Lab
Shanghai Key Laboratory of New Drug Design
School of Pharmacy
East China University of Sci. & Tech.
Room 527, Building 18, 130 Meilong Road,
Shanghai, 200237, P. R. China
Tel: (86) 21 6425 0213
Prof. Honglin Li
hlli@ecust.edu.cn

Copyright © 2019 Prof. HongLin Li's Group, School of Pharmacy, East China University of Science & Technology · All Right Reserved.
沪ICP备19004698号-1 |  沪公网安备31011302004713号