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

Protein-protein Interfaces02:04

Protein-protein Interfaces

15.0K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
15.0K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

15.0K
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...
15.0K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.2K
2.2K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

3.1K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
3.1K
Protein and Protein Structures02:15

Protein and Protein Structures

20.1K
20.1K
Protein Networks02:26

Protein Networks

4.7K
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,...
4.7K

You might also read

Related Articles

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

Sort by
Same author

Multi-omics mechanistic investigation of Yograj Guggulu, an Ayurvedic polyherbal formulation, against MIA-induced osteoarthritis in rats.

Journal of ethnopharmacology·2026
Same author

Antimicrobial peptide-induced inner membrane hyperpolarization is associated with antibiotic sensitization and attenuated MIC escalation in multidrug-resistant Gram-negative pathogens.

npj antimicrobials and resistance·2026
Same author

Electric Field Directed Structural Modulation and Nanoassembly of Peptide Hydrogels.

Langmuir : the ACS journal of surfaces and colloids·2026
Same author

Functional Modulation of Peptide Structural Interaction Fingerprints upon Stereochemical Diversification.

The journal of physical chemistry. B·2025
Same author

Computational protein design: Advancing biotechnology through in silico engineering.

Progress in biophysics and molecular biology·2025
Same author

Peptide-Based Catalyst Mimicking Hydrolase Enzyme.

Journal of peptide science : an official publication of the European Peptide Society·2025
Same journal

Translational synthetic biology.

Systems and synthetic biology·2017
Same journal

Evolving modular genetic regulatory networks with a recursive, top-down approach.

Systems and synthetic biology·2017
Same journal

Exploring the differences in metabolic behavior of astrocyte and glioblastoma: a flux balance analysis approach.

Systems and synthetic biology·2017
Same journal

The synthetic biology puzzle: a qualitative study on public reflections towards a governance framework.

Systems and synthetic biology·2017
Same journal

The role of CRKL in breast cancer metastasis: insights from systems biology.

Systems and synthetic biology·2017
Same journal

Predicting stable functional peptides from the intergenic space of <i>E. coli</i>.

Systems and synthetic biology·2017
See all related articles

Related Experiment Video

Updated: Apr 3, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K

bPE toolkit: toolkit for computational protein engineering.

Gaurav Jerath1, Prakash Kishore Hazam1, Vibin Ramakrishnan1

  • 1Department of Biotechnology, Indian Institute of Technology, Guwahati, 781039 India.

Systems and Synthetic Biology
|September 24, 2015
PubMed
Summary
This summary is machine-generated.

This study introduces a computational toolkit with five essential programs for analyzing protein structure files. These tools facilitate basic operations like chirality checks and energy calculations for protein characterization.

Keywords:
Protein designProtein engineeringProtein structureToolkit

More Related Videos

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

1.3K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

2.7K

Related Experiment Videos

Last Updated: Apr 3, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K
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

1.3K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

2.7K

Area of Science:

  • Structural bioinformatics
  • Computational chemistry
  • Biophysics

Background:

  • Protein structure analysis is crucial for understanding biological function.
  • Existing tools may lack comprehensive basic operations for PDB files.
  • Efficient computational methods are needed for protein characterization.

Purpose of the Study:

  • To introduce a versatile computational toolkit for protein structure analysis.
  • To provide five distinct utility tools for common operations on PDB files.
  • To enable integration into existing bioinformatics pipelines or standalone use.

Main Methods:

  • Development of a toolkit comprising five specialized programs: ProChiral, CoMa, DaRe, HyPE, and EsInE.
  • Implementation of algorithms for chirality checking, contact map generation, data redundancy assessment, and energy calculations (hydrogen bond and electrostatic interactions).
  • Packaging these tools for accessibility as a downloadable resource.

Main Results:

  • Successful creation of a computational toolkit with five functional utility programs.
  • Demonstrated utility for basic operations on protein structure files (PDB format).
  • Provided tools for specific analyses including ProChiral, CoMa, DaRe, HyPE, and EsInE.

Conclusions:

  • The presented toolkit offers a valuable resource for computational protein structure characterization.
  • The five programs can be used independently or integrated into larger analysis workflows.
  • The toolkit is accessible for download, promoting its adoption in research.