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

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

18.2K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
18.2K
Protein-protein Interfaces02:04

Protein-protein Interfaces

13.4K
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...
13.4K
Protein Networks02:26

Protein Networks

4.1K
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,...
4.1K
Protein Organization01:24

Protein Organization

7.2K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
7.2K
Conserved Binding Sites01:49

Conserved Binding Sites

4.4K
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...
4.4K
Ligand Binding Sites02:40

Ligand Binding Sites

13.3K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
13.3K

You might also read

Related Articles

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

Sort by
Same author

A Risk-Tiered Validation Framework for Artificial Intelligence in Drug Discovery: From Reproducibility to Clinical Translation.

International journal of molecular sciences·2026
Same author

Quantum Computing and Quantum Technologies in Drug Discovery and Therapeutics: Evidence, Benchmarking, and Translational Integration.

Drug design, development and therapy·2026
Same author

Therapeutic Alternatives to Recombinant Biologics: Mechanistic Framework, Clinical Evidence, and Selection Guidance.

Drug design, development and therapy·2026
Same author

Quantum mechanics in drug design: Progress, challenges, and future frontiers.

Communicative & integrative biology·2025
Same author

Artificial Intelligence in Small-Molecule Drug Discovery: A Critical Review of Methods, Applications, and Real-World Outcomes.

Pharmaceuticals (Basel, Switzerland)·2025
Same author

Engineering Universal Cancer Immunity: Non-Tumor-Specific mRNA Vaccines Trigger Epitope Spreading in Cold Tumors.

Vaccines·2025

Related Experiment Video

Updated: Sep 16, 2025

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

2.0K

FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.

Sarfaraz K Niazi1

  • 1College of Pharmacy, University of Illinois, Chicago, IL 60612, USA.

International Journal of Molecular Sciences
|July 12, 2025
PubMed
Summary

FINCHES is a computational framework for predicting protein interactions in disordered regions. It offers rapid, sequence-based analysis without simulations, advancing our understanding of protein function.

Keywords:
AWSEMFINCHESforce fieldintermolecular interactionintrinsic disordermolecular dynamicsproteins

More Related Videos

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

17.2K
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

369

Related Experiment Videos

Last Updated: Sep 16, 2025

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

2.0K
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

17.2K
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

369

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Intrinsically disordered regions (IDRs) play crucial roles in cellular functions but are challenging to study due to their dynamic nature.
  • Predicting intermolecular interactions in IDRs is vital for understanding protein function and dysfunction.
  • Existing computational methods often require molecular simulations, limiting speed and accessibility.

Purpose of the Study:

  • To review the FINCHES (Force field-based Interaction Network for Characterizing Heterotypic and Entropic Sequences) computational framework.
  • To evaluate FINCHES's capabilities for rapid, sequence-based prediction of IDR interactions.
  • To compare FINCHES with other computational approaches for IDR analysis.

Main Methods:

  • Review of the FINCHES framework and its underlying principles.
  • Comparative analysis of FINCHES against other computational methods.
  • Discussion of experimental validation strategies for IDR interaction predictions.

Main Results:

  • FINCHES enables rapid, sequence-based prediction of intermolecular interactions in IDRs.
  • The framework bypasses the need for computationally intensive molecular simulations.
  • Detailed comparisons highlight FINCHES's strengths and limitations relative to existing tools.

Conclusions:

  • FINCHES presents a significant advancement in computationally modeling IDR interactions.
  • The framework has the potential to accelerate research into disordered protein function.
  • Further development and validation are essential for robust application in complex biological systems.