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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.1K
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...
11.1K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.2K
3.2K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
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...
4.3K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

44.0K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
44.0K
Overview of Advanced Functional Groups02:22

Overview of Advanced Functional Groups

24.6K

Functional groups are groups of atoms with specific chemical properties that occur within organic molecules and are sometimes denoted as “R”. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of Advanced Functional Groups
The table below summarizes some of the major functional groups in organic chemistry.
24.6K
Protein Folding01:22

Protein Folding

118.8K
Overview
118.8K

You might also read

Related Articles

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

Sort by
Same author

ECOD: Classification of domains in AFDB Swiss-Prot structure predictions.

PLoS computational biology·2026
Same author

Genomic Signatures of Speciation in Butterflies.

Systematic biology·2026
Same author

Modeling the structure-conditioned sequence landscape for large-scale protein design with TriFlow.

bioRxiv : the preprint server for biology·2025
Same author

Exploring the Terra incognita of AI-based domain classifications.

Protein science : a publication of the Protein Society·2025
Same author

NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT.

Science (New York, N.Y.)·2025
Same author

Assessment of Protein Complex Predictions in CASP16: Are We Making Progress?

Proteins·2025
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Related Experiment Video

Updated: Aug 16, 2025

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
06:29

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Published on: March 3, 2021

5.6K

DPAM: A domain parser for AlphaFold models.

Jing Zhang1,2,3, R Dustin Schaeffer2, Jesse Durham1,2,3

  • 1Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Protein Science : a Publication of the Protein Society
|December 20, 2022
PubMed
Summary
This summary is machine-generated.

A new tool, Domain Parser for AlphaFold Models (DPAM), automatically identifies protein domains in AlphaFold structures. This computational advancement aids in classifying vast protein structure data for functional and evolutionary insights.

Keywords:
domain classificationdomain parserprotein domainsstructural predictions

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K
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

1.9K

Related Experiment Videos

Last Updated: Aug 16, 2025

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
06:29

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Published on: March 3, 2021

5.6K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K
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

1.9K

Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • AlphaFold has revolutionized protein structure prediction, generating millions of high-accuracy models.
  • Classifying protein domains within these models is crucial for understanding protein function and evolution.
  • Existing classification systems face challenges processing the scale of AlphaFold data.

Purpose of the Study:

  • To develop an automated computational tool for parsing and classifying protein domains from AlphaFold models.
  • To improve the efficiency and accuracy of domain assignment compared to existing methods.

Main Methods:

  • The Domain Parser for AlphaFold Models (DPAM) utilizes inter-residue distances and predicted aligned errors.
  • It incorporates sequence (HHsuite) and structural (Dali) similarity searches against the Evolutionary Classification of protein Domains (ECOD) database.
  • DPAM identifies globular domains within 3D structures.

Main Results:

  • DPAM achieved 98.8% domain recognition accuracy on a benchmark dataset of 18,759 AlphaFold models.
  • It correctly assigned domain boundaries in 87.5% of cases.
  • DPAM significantly outperformed existing structure-based and homology-based domain assignment methods.

Conclusions:

  • DPAM provides an efficient and accurate automated solution for classifying protein domains from large-scale AlphaFold structural models.
  • This tool facilitates the extraction of evolutionary context and functional insights from predicted protein structures.
  • DPAM is essential for leveraging the full potential of the AlphaFold Database for biological research.