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 Organization01:24

Protein Organization

6.6K
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....
6.6K
Per-Unit Sequence Models01:26

Per-Unit Sequence Models

93
An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...
93
Protein and Protein Structure02:15

Protein and Protein Structure

79.7K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
79.7K
Protein and Protein Structures02:15

Protein and Protein Structures

10.6K
10.6K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.9K
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...
10.9K
Introduction to Structures01:30

Introduction to Structures

1.1K
A structure is defined as a system of interconnected members designed to support or transfer forces and successfully withstand the loads acting on them. The internal forces of a structure can be determined by decomposing the structure and analyzing the free-body diagrams of the individual members or of a combination of members. This helps in understanding the structural elements' behavior and ensuring that the structure is stable and can withstand the subjected loads.
There are three main...
1.1K

You might also read

Related Articles

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

Sort by
Same author

Defective cuticle-derived signals enhance extracellular ATP response and plant immunity.

The New phytologist·2026
Same author

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs.

Briefings in bioinformatics·2026
Same author

Evaluating AlphaFold Tools and Related Scoring Functions for Protein-peptide Complex Prediction.

Genomics, proteomics & bioinformatics·2026
Same author

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data.

Biomolecules·2025
Same author

Phloem-specific translational regulation of soybean nodulation: Insights from a phloem-targeted TRAP-seq approach.

Plant physiology·2025
Same author

Ad hoc, post hoc and intrinsic-hoc in bioinformatics.

Nature biotechnology·2025
Same journal

A human-specific genetic modifier reconfigures large-scale cortical network dynamics underlying behavioral performance.

bioRxiv : the preprint server for biology·2026
Same journal

<i>Staphylococcus aureus</i> uses a eukaryotic-like uridyltransferase to make UDP-GlcNAc for cell wall synthesis.

bioRxiv : the preprint server for biology·2026
Same journal

Dynamic redistribution of eIF4F controls cap-dependent translation initiation.

bioRxiv : the preprint server for biology·2026
Same journal

When does additional information improve accuracy of RNA secondary structure prediction?

bioRxiv : the preprint server for biology·2026
Same journal

Normative brain-state trajectories reveal deviation from healthy aging in Alzheimer's disease.

bioRxiv : the preprint server for biology·2026
Same journal

Noradrenergic infraslow rhythm during sleep is the critical link between heart-rate dynamics and memory consolidation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Jul 18, 2025

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

68.7K

S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure.

Duolin Wang, Mahdi Pourmirzaei, Usman L Abbas

    Biorxiv : the Preprint Server for Biology
    |August 23, 2023
    PubMed
    Summary
    This summary is machine-generated.

    We developed S-PLM, a novel 3D structure-aware protein language model (PLM) that integrates protein sequence and structure data. This approach enhances protein function prediction and design capabilities beyond traditional sequence-only models.

    More Related Videos

    Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
    07:08

    Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

    Published on: July 14, 2015

    7.3K
    Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
    09:51

    Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

    Published on: July 16, 2017

    15.5K

    Related Experiment Videos

    Last Updated: Jul 18, 2025

    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

    68.7K
    Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
    07:08

    Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

    Published on: July 14, 2015

    7.3K
    Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
    09:51

    Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

    Published on: July 16, 2017

    15.5K

    Area of Science:

    • Computational Biology
    • Structural Bioinformatics
    • Machine Learning in Biology

    Background:

    • Large protein language models (PLMs) are revolutionizing protein research, aiding in function determination and protein design.
    • Current PLMs primarily rely on protein sequences, often neglecting crucial 3D structural information.
    • This omission limits the predictive power of PLMs for structure-dependent biological and engineering applications.

    Conclusions:

    • Integrating 3D structural information into protein language models significantly enhances their predictive capabilities.
    • S-PLM offers a powerful and adaptable framework for advancing protein research and engineering.
    • The developed S-PLM and associated tools are publicly available to the research community.