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

GPI Anchoring of Proteins in the ER Membrane01:29

GPI Anchoring of Proteins in the ER Membrane

GPI-anchoring is a post-translational, reversible protein modification that is ubiquitous in eukaryotes. Such proteins are primarily present on the exoplasmic leaflet of the plasma membrane.
GPI-anchor structure
A sequence of 11 enzymatic reactions results in the synthesis of the complete GPI anchor consisting of a hydrophobic and a hydrophilic portion. The hydrophobic portion comprises phosphatidylinositol, while the hydrophilic part comprises polar groups like phosphoethanolamine,...
Lipids as Anchors01:32

Lipids as Anchors

In the plasma membrane, the lipids forming the bilayer can also act as an anchor to tether proteins to the membrane. The three main types of lipid anchors found in eukaryotes are – prenyl groups, fatty acyl groups, and glycosylphosphatidylinositol or GPI groups. Prenyl and fatty acyl groups act as anchors on the cytosolic surface of the membrane, whereas GPI anchors proteins on the extracellular side.
The carboxy-terminal of most of the prenylated proteins, such as Ras proteins, contains the...
End Point Prediction: Gran Plot01:07

End Point Prediction: Gran Plot

A Gran plot is used to predict the equivalence volume or endpoint of a potentiometric or acid-base titration without reaching the endpoint. Typically, titration data is collected as a function of the titrant's volume up to a point less than the equivalence volume and then transformed into a linear format. The straight line is extended to the x-axis, indicating the necessary titrant volume to achieve the equivalence point.
For potentiometric titration, the Gran plot is created by plotting the...
Prediction Intervals01:03

Prediction Intervals

The interval estimate of any variable is known as the prediction interval. It helps decide if a point estimate is dependable.
However, the point estimate is most likely not the exact value of the population parameter, but close to it. After calculating point estimates, we construct interval estimates, called confidence intervals or prediction intervals. This prediction interval comprises a range of values unlike the point estimate and is a better predictor of the observed sample value, y. 
The...
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
Anchoring Junctions01:03

Anchoring Junctions

Anchoring junctions are multiprotein complexes that help cells connect to other cells and the extracellular matrix. Anchoring junctions are present on the lateral and basal surfaces of cells, providing strong and flexible connections. Focal adhesions are often formed due to cell interactions with the ECM substrata, which initiate signal transduction via kinase cascades and other mechanisms. Together, they provide stability and tissue integrity. There are three types of anchoring junctions:...

You might also read

Related Articles

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

Sort by
Same author

Computational Resources for Molecular Biology 2026.

Journal of molecular biology·2026
Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026
Same author

Alpha&ESMhFolds: An Updated Web Server for the Comparison, Evaluation, and Annotation of Human AlphaFold2 and ESMFold Models.

Journal of molecular biology·2026
Same author

<i>Acinetobacter</i> enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.

mSphere·2026
Same author

Understanding the evolutionary dynamics of Monkeypox virus through less explored pathways.

Scientific reports·2025
Same author

Predicting the Pathogenicity of Human Protein Variants: Not Only a Matter of Residue Labeling.

Methods in molecular biology (Clifton, N.J.)·2025
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jun 30, 2026

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

PredGPI: a GPI-anchor predictor.

Andrea Pierleoni1, Pier Luigi Martelli, Rita Casadio

  • 1Biocomputing Group, Department of Biology, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy. andrea@biocomp.unibo.it

BMC Bioinformatics
|September 25, 2008
PubMed
Summary
This summary is machine-generated.

PredGPI accurately predicts Glycosylphosphatidylinositol (GPI) anchors and their cleavage sites in proteins. This computational tool improves proteome annotation by offering a rapid and precise method for identifying GPI-anchored proteins.

More Related Videos

Installation Method to Enhance Quality Control for Fiber Reinforced Polymer Spike Anchors
06:21

Installation Method to Enhance Quality Control for Fiber Reinforced Polymer Spike Anchors

Published on: April 10, 2018

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: Jun 30, 2026

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Installation Method to Enhance Quality Control for Fiber Reinforced Polymer Spike Anchors
06:21

Installation Method to Enhance Quality Control for Fiber Reinforced Polymer Spike Anchors

Published on: April 10, 2018

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Eukaryotic proteins on the plasma membrane's extracellular side often have a Glycosylphosphatidylinositol (GPI) anchor.
  • This anchor attaches to the C-terminal residue post-proteolytic cleavage at the omega-site.
  • Existing computational methods for predicting GPI anchors need improvement for whole proteome analysis.

Purpose of the Study:

  • To develop an accurate computational method for predicting GPI anchors and omega-site locations.
  • To enhance the reliability of proteome annotation for GPI-anchored proteins.

Main Methods:

  • Developed PredGPI, a novel prediction method.
  • Coupled a Hidden Markov Model (HMM) with a Support Vector Machine (SVM).
  • Trained PredGPI on a curated, non-redundant dataset of experimentally verified GPI-anchored proteins.

Main Results:

  • PredGPI efficiently predicts both the presence of GPI anchors and the omega-site position.
  • The method demonstrates superior performance compared to existing prediction tools.
  • Achieved a lower false positive rate than other available methods.

Conclusions:

  • PredGPI offers a cost-effective, rapid, and accurate approach for screening entire proteomes.
  • The method successfully replicates findings from high-throughput experiments.
  • Enhances the annotation of GPI-anchored proteins in large-scale studies.