Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Conserved Binding Sites

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...

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

Predicting Products: SN1 vs. SN2

Predicting Products: S_N1 vs. S_N2

Nucleophilic substitution reactions of alkyl halides can proceed via an SN1 or an SN2 mechanism. While in SN2 reactions, the nucleophile attacks the substrate simultaneously as the leaving group departs, in SN1 reactions, the substrate first dissociates to give the carbocation intermediate. Various factors such as the structure of the substrate, the strength of the nucleophile, and the nature of the solvent promote one mechanism over the other.
With increased substitution on the alkyl halide,...

Predicting Reaction Outcomes

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,...

You might also read

Related Articles

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

Sort by

Same author

Are Children Like Werewolves? Full Moon and Its Association with Sleep and Activity Behaviors in an International Sample of Children.

Frontiers in pediatrics·2016

Same author

MAP30 inhibits autophagy through enhancing acetyltransferase p300 and induces apoptosis in acute myeloid leukemia cells.

Oncology reports·2016

Same author

Fluoxetine protects against IL-1β-induced neuronal apoptosis via downregulation of p53.

Neuropharmacology·2016

Same author

Physical activity, sedentary behaviors and risk of gestational diabetes mellitus: a population-based cross-sectional study in Tianjin, China.

European journal of endocrinology·2016

Same author

Building Structured Personal Health Records from Photographs of Printed Medical Records.

AMIA ... Annual Symposium proceedings. AMIA Symposium·2016

Same author

AEG-1/MTDH-activated autophagy enhances human malignant glioma susceptibility to TGF-β1-triggered epithelial-mesenchymal transition.

Oncotarget·2016

Search research articles

Related Experiment Video

Updated: Mar 10, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

PrAS: Prediction of amidation sites using multiple feature extraction.

Tong Wang¹, Wei Zheng¹, Qiqige Wuyun¹

¹School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China.

Computational Biology and Chemistry

|December 6, 2016

Summary

This study introduces PrAS, a new computational tool for predicting protein amidation sites. PrAS offers a faster, more cost-effective alternative to experimental methods for identifying these crucial biological markers.

Keywords:

Amidation sites Positive contribution feature selection Posttranslational modification (PTM)Support vector machine (SVM)

More Related Videos

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Related Experiment Videos

Last Updated: Mar 10, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Area of Science:

Biochemistry
Computational Biology
Bioinformatics

Background:

Protein amidation is implicated in critical diseases such as neural dysfunction and hypertension.
Experimental identification of amidation sites is resource-intensive and time-consuming.

Purpose of the Study:

To develop and present PrAS (Prediction of Amidation Sites), the first software package for academic users to predict protein amidation sites.
To offer an efficient and cost-effective computational approach for identifying amidation sites.

Main Methods:

Incorporated four feature types: position-based, physicochemical/biochemical properties, predicted structure-based, and evolutionary information.
Utilized a novel positive contribution feature selection method for feature optimization.

Main Results:

PrAS achieved high performance on an independent test set with an AUC of 0.96.
Demonstrated excellent accuracy (92.1%), sensitivity (81.2%), specificity (94.9%), and MCC (0.76).

Conclusions:

PrAS provides a robust and efficient computational tool for predicting protein amidation sites.
The developed predictor significantly advances the field by offering a practical solution for researchers.