Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

IR Frequency Region: Fingerprint Region01:03

IR Frequency Region: Fingerprint Region

IR spectra are divided into two main regions: the diagnostic region and the fingerprint region. The diagnostic region of the spectrum lies above 1500 cm−1. The absorptions resulting from single-bond vibrations of the N–H, C–H, and O–H stretch at higher wavenumbers and appear on the left side of the spectrum. The stretching absorptions of the C≡C and C≡N occur between 2100–2300 cm−1. In contrast, those arising from stretching absorptions of the C=O, C=N, and C=C occur between 1600–1850 cm−1.
The...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Development of 2,8-diazaspiro[4.5]decan-3-ones as novel sigma-1 receptor antagonists and evaluation of antihyperalgesic effects.

Bioorganic chemistry·2026
Same author

Structure-guided discovery of 1H-pyrazolo[3,4-c]pyridin-3-amines as a novel class of hematopoietic progenitor kinase 1 (HPK1) inhibitors.

European journal of medicinal chemistry·2026
Same author

Ultrasound-programmable tumor extracellular vesicles delivery system for dual immune-epigenetic therapy against colorectal cancer metastasis.

Journal of controlled release : official journal of the Controlled Release Society·2026
Same author

Combined Microbiome and Metabolomic Analyses Reveal That Fine-Root Invasion of <i>Rhododendron auriculatum</i> Sapling Enhances Microbial Decomposition of <i>Sphagnum palustre</i> L.

Microorganisms·2026
Same author

Structural basis of the neuronal M-current generated by an asymmetric KCNQ2/3 assembly.

Cell research·2026
Same author

Cryo-EM Structure of the TRPC1/5 Heteromer Enables Design of Antidepressant and Anxiolytic Drug with Reduced Side Effects.

Nature communications·2026

Related Experiment Video

Updated: Jun 16, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

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

Bing Xiong1, Jie Wu, David L Burk

  • 1State 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. bxiong@mail.shcnc.ac.cn

BMC Bioinformatics
|January 27, 2010
PubMed
Summary

We developed BSSF, an ultrafast method for identifying similar binding sites in protein structures. This tool aids drug design and structural genomics by analyzing sequence-structure-function relationships.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy
08:10

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy

Published on: November 20, 2021

Related Experiment Videos

Last Updated: Jun 16, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy
08:10

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy

Published on: November 20, 2021

Area of Science:

  • Genomics
  • Structural Biology
  • Bioinformatics

Background:

  • Advancements in genomics and structural genomics necessitate improved methods for understanding gene and protein function.
  • Current sequence/structure-based methods have limitations in fully deciphering the sequence-structure-function relationship.

Purpose of the Study:

  • To introduce BSSF (Binding Site Similarity & Function), an ultrafast computational method for similarity searching within a 3D binding site database.
  • To enable researchers to infer functions of novel genes and proteins.

Main Methods:

  • Utilizes a fingerprint representation of binding sites for similarity searches.
  • Employs a validated statistical Z-score function to assess similarity, even within sub-pockets.
  • Fingerprint-based similarity measurement validated against geometric hashing, a standard 3D method.

Main Results:

  • BSSF demonstrates high speed and accuracy in identifying similar binding sites.
  • The method effectively handles similarities within specific sub-pockets.
  • Database searches provide statistical insights into Gene Ontology terms and Enzyme Commission numbers.

Conclusions:

  • The web-based BSSF system accelerates drug design and structural genomics research.
  • Facilitates identification of similar binding sites and provides functional insights through hit list analysis.