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...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Mechanical Protein Functions

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.

Structural Protein Function

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to...

Structural Protein Function

Structural Protein Function

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

You might also read

Related Articles

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

Sort by

Same author

Beyond Random Splits: Assessing the Generalization of Graph and Vector Models for WT-Structure-Only Drug Resistance Prediction under Protein-Disjoint Evaluation.

Computational and structural biotechnology journal·2026

Same author

A Molecular-Protein Fusion Framework for Rapid Virtual Screening: Accelerating Lead Discovery for "Undruggable'' Oncogenic Targets.

Pharmaceuticals (Basel, Switzerland)·2026

Same author

Paean: A Unified and Efficient Transcriptome Quantification System Using Heterogeneous Computing.

Journal of molecular biology·2026

Same author

SenolyticSynergy: An Attention-Based Network for Discovering Novel Senolytic Combinations via Human Aging Genomics.

International journal of molecular sciences·2025

Same author

Enhancing Chitosanase Activity via Directed Evolution and Its Molecular Mechanisms.

Journal of agricultural and food chemistry·2025

Same author

Phase Separation-Mediated Multienzyme Assembly In Vivo.

Journal of agricultural and food chemistry·2025

Search research articles

Related Experiment Video

Updated: Feb 9, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Sequence-based prediction of physicochemical interactions at protein functional sites using a

Min Han¹, Yifan Song¹, Jiaqiang Qian¹

¹Department of Physiology and Biophysics, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.

BMC Bioinformatics

|June 3, 2018

Summary

A new sequence-based method accurately predicts protein functional sites and their physicochemical interactions, aiding drug design. This approach enhances understanding of protein evolution and function.

Keywords:

Domain profile module Hidden Markov model Physicochemical interaction prediction Protein functional site prediction fiDPD

More Related Videos

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Related Experiment Videos

Last Updated: Feb 9, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Area of Science:

Biochemistry and Molecular Biology
Bioinformatics
Computational Biology

Background:

Identifying protein functional sites (PFSs) and their associated physicochemical interactions is crucial for understanding protein function and biochemical processes.
Existing knowledge-based methods are limited in accurately predicting these physicochemical interactions at PFSs.

Purpose of the Study:

To develop and present a novel sequence-based method for predicting physicochemical interactions at PFSs.
To provide a tool for rational drug design and side-effect assessment.

Main Methods:

Developed a sequence-based method utilizing a functional site and physicochemical interaction-annotated domain profile database (fiDPD).
The fiDPD database was constructed using protein domains from the Protein Data Bank.
Applied the method to 13 target proteins from the Critical Assessment of Structure Prediction (CASP10/11).

Main Results:

Achieved a Matthews correlation coefficient (MCC) of 0.66 for PFS prediction.
Obtained an 80% recall in predicting associated physicochemical interactions.
Demonstrated that physical interactions at PFSs are conserved during protein evolution.

Conclusions:

The developed method offers a valuable sequence-based tool for predicting physicochemical interactions at PFSs.
The findings suggest evolutionary conservation of physical interactions at protein functional sites.
The tool is freely available for applications in rational drug design and side-effect assessment.