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Open Access Methodology article

BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server

Bing Xiong1*, Jie Wu2, David L Burk3, Mengzhu Xue1, Hualiang Jiang1 and Jingkang Shen1*

Author Affiliations

1 State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai, 201203, PR China

2 Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA

3 Department of Biochemistry, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 1A4, Canada

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BMC Bioinformatics 2010, 11:47  doi:10.1186/1471-2105-11-47

Published: 25 January 2010



Genome sequencing and post-genomics projects such as structural genomics are extending the frontier of the study of sequence-structure-function relationship of genes and their products. Although many sequence/structure-based methods have been devised with the aim of deciphering this delicate relationship, there still remain large gaps in this fundamental problem, which continuously drives researchers to develop novel methods to extract relevant information from sequences and structures and to infer the functions of newly identified genes by genomics technology.


Here we present an ultrafast method, named BSSF(Binding Site Similarity & Function), which enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method. After conducting the database searching, the hit list is further analyzed to provide basic statistical information about the occurrences of Gene Ontology terms and Enzyme Commission numbers, which may benefit researchers by helping them to design further experiments to study the query proteins.


This ultrafast web-based system will not only help researchers interested in drug design and structural genomics to identify similar binding sites, but also assist them by providing further analysis of hit list from database searching.