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

10.8K
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...
10.8K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

43.3K
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...
43.3K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.1K
3.1K
Atomic Force Microscopy01:08

Atomic Force Microscopy

3.3K
Atomic force microscopy (AFM) is a type of scanning probe microscopy that can analyze topographic details of various specimens like ceramics, glass, polymers, and biological samples. AFM offers over 1000 times more resolution than the optical imaging system. Images generated from AFM are three-dimensional surface profiles, offering an advantage over the flat, two-dimensional images from other imaging techniques.
The AFM Probe
The probe is regarded as the heart of any AFM setup and comprises the...
3.3K
Amides to Amines: LiAlH4 Reduction01:20

Amides to Amines: LiAlH4 Reduction

4.5K
Amide reduction with strong reducing agents like lithium aluminum hydride proceeds through a nucleophilic acyl substitution to form amines. Primary, secondary, and tertiary amides yield primary, secondary, and tertiary amines, respectively.
Amide reduction requires two equivalents of the reducing agent, acting as a source of hydride ions. As shown in the figure, the reaction is initiated with a nucleophilic attack by the hydride ion at the carbonyl carbon to form a tetrahedral intermediate.
4.5K

You might also read

Related Articles

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

Sort by
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 author

Assessment of Nucleic Acid Structure Prediction in CASP16.

Proteins·2025
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Jun 5, 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

1.7K

DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence.

Jesse Durham1,2,3, Jing Zhang1,2,3, Richard D Schaeffer3,4

  • 1Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States.

Bioinformatics (Oxford, England)
|December 13, 2024
PubMed
Summary
This summary is machine-generated.

A new AI tool, DPAM-AI, accurately segments protein structures from the AlphaFold Protein Structure Database (AFDB) into evolutionary domains. This advances understanding of protein function by refining domain boundaries and identifying multi-unit domains.

More Related Videos

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

5.4K
Novel Atomic Force Microscopy Based Biopanning for Isolation of Morphology Specific Reagents against TDP-43 Variants in Amyotrophic Lateral Sclerosis
13:31

Novel Atomic Force Microscopy Based Biopanning for Isolation of Morphology Specific Reagents against TDP-43 Variants in Amyotrophic Lateral Sclerosis

Published on: February 12, 2015

8.7K

Related Experiment Videos

Last Updated: Jun 5, 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

1.7K
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

5.4K
Novel Atomic Force Microscopy Based Biopanning for Isolation of Morphology Specific Reagents against TDP-43 Variants in Amyotrophic Lateral Sclerosis
13:31

Novel Atomic Force Microscopy Based Biopanning for Isolation of Morphology Specific Reagents against TDP-43 Variants in Amyotrophic Lateral Sclerosis

Published on: February 12, 2015

8.7K

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The AlphaFold Protein Structure Database (AFDB) provides 200 million near-atomic resolution protein structures, covering nearly the entire protein universe.
  • Segmenting protein models into domains and classifying them evolutionarily is crucial for understanding protein function.

Purpose of the Study:

  • To introduce DPAM-AI, an Artificial Intelligence-based Domain Parser for AlphaFold Models.
  • To accurately delineate and classify protein domains within the vast AFDB dataset.

Main Methods:

  • DPAM-AI employs a convolutional neural network trained on the Evolutionary Classification Of protein Domains (ECOD) database.
  • It integrates inter-residue distances, predicted aligned errors, and sequence/structural alignments.
  • Utilizes HHsuite and Dali for similarity searches to detect previously classified domains.

Main Results:

  • DPAM-AI demonstrated superior performance against benchmark sets compared to DPAM, Merizo, and Chainsaw.
  • Applied to Pfam-classified proteins in AFDB, DPAM-AI obtained representative 3D structures for 89% of families.
  • Uncovered that 15% of Pfam domains contain multiple structural/evolutionary units and refined boundaries for over half.

Conclusions:

  • DPAM-AI effectively segments protein domains within the AFDB, providing valuable structural and evolutionary insights.
  • The tool refines domain boundaries and identifies complex multi-unit domains, enhancing our understanding of protein architecture and function.