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

You might also read

Related Articles

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

Sort by
Same author

A highly efficient method to differentiate CGRP-expressing peptidergic nociceptors from human induced pluripotent stem cells.

Stem cell reports·2026
Same author

GWAS of extended prescription analgesic use identifies genetic loci in chronic pain.

Nature communications·2026
Same author

Spatial Mapping of Genetic Liability to Psychiatric Disorders in the Adult Human Hippocampus.

Biological psychiatry global open science·2026
Same author

Using targeted therapy to promote a pro-inflammatory tumour microenvironment and anti-tumour immune response in high grade serous ovarian cancer.

British journal of cancer·2026
Same author

Ethical dilemmas in climate change and healthcare delivery: a cross-sectional survey of US patient perspectives.

BMC medicine·2026
Same author

Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish its interaction with the Ser/Thr kinase CK1α.

Open biology·2026

Related Experiment Video

Updated: Jul 5, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a

Thomas P Walsh1, Caleb Webber, Stephen Searle

  • 1College of Life Sciences, University of Dundee, Dundee, UK.

Nucleic Acids Research
|May 27, 2008
PubMed
Summary

SCANPS offers sensitive and selective protein domain searching, outperforming PSI-BLAST. Its web server provides rapid searches of large databases, including SCOP, with enhanced result visualization.

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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Related Experiment Videos

Last Updated: Jul 5, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein domain identification is crucial for understanding protein function and evolution.
  • Existing methods like PSI-BLAST have limitations in sensitivity and selectivity for domain searching.
  • Computational efficiency is a key challenge in large-scale sequence database searches.

Purpose of the Study:

  • To introduce SCANPS, a novel iterative profile searching tool for protein domain identification.
  • To evaluate SCANPS's performance against existing methods, particularly PSI-BLAST.
  • To provide a user-friendly web server for accessing SCANPS capabilities.

Main Methods:

  • SCANPS employs full dynamic programming in each iterative cycle and on-the-fly significance estimation.
  • It utilizes on-chip (MMX, SSE2) and MPI parallelism to accelerate computation.
  • A web server integrates SCANPS with updated protein sequence databases, including SCOP.

Main Results:

  • SCANPS demonstrates superior sensitivity and selectivity compared to PSI-BLAST in domain-searching benchmarks.
  • Despite computational intensity, SCANPS achieves acceptable search times on large databases.
  • The web server facilitates rapid searches and offers a novel tree-based visualization for SCOP results.

Conclusions:

  • SCANPS represents a significant advancement in sensitive and selective protein domain identification.
  • The SCANPS web server enhances accessibility and usability for researchers.
  • The new visualization aids in interpreting domain classifications and relationships within the SCOP hierarchy.