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

Improving Translational Accuracy02:07

Improving Translational Accuracy

11.5K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.5K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K
Per-Unit Sequence Models01:26

Per-Unit Sequence Models

87
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...
87
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
Protein Complex Assembly02:41

Protein Complex Assembly

2.1K
2.1K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K

You might also read

Related Articles

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

Sort by
Same author

TransKla: A Local-Global Cross-Attention Based Transformer Approach for Prediction of Lysine Lactylation Sites.

Journal of chemical information and modeling·2026
Same author

DrugDL: dual-modal deep learning framework for multi-property drug prediction and targeted therapy discovery.

Bioinformatics (Oxford, England)·2026
Same author

Cell type annotation for scATAC-seq via DNA large language model and graph domain adaptation.

PLoS computational biology·2026
Same author

Mamba-ACP: a Hybrid State-Space and Transformer Framework for Interpretable Anticancer Peptide Prediction.

IEEE transactions on computational biology and bioinformatics·2026
Same author

SGLEPocket: A Spatial Gating and Local Feature Enhancement Network for Protein-Ligand Binding Pocket Prediction.

Journal of chemical information and modeling·2026
Same author

Leveraging Residual Graph Convolutional Networks with Cross-Attention Mechanisms for High-Accuracy Protein Function Prediction.

Journal of chemical information and modeling·2026

Related Experiment Video

Updated: Jul 15, 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

Integrating unsupervised language model with multi-view multiple sequence alignments for high-accuracy inter-chain

Zi Liu1, Yi-Heng Zhu2, Long-Chen Shen3

  • 1School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing, 210094, China; Computer Department, Jingdezhen Ceramic University, Jingdezhen, 333403 , China.

Computers in Biology and Medicine
|September 25, 2023
PubMed
Summary
This summary is machine-generated.

ICCPred, a new deep learning method, accurately predicts protein inter-chain contacts using amino acid sequences. This approach enhances understanding of protein complex structures and functions.

Keywords:
Co-evolution diversityDeep residual networksInter-chain contact predictionMultiple sequence alignmentPre-trained language 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
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K

Related Experiment Videos

Last Updated: Jul 15, 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
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Accurate identification of inter-chain contacts is crucial for determining protein complex 3D structures and biological functions.
  • Existing methods for predicting inter-chain contacts from amino acid sequences have limitations.

Purpose of the Study:

  • To develop a novel deep learning method, ICCPred, for accurate prediction of inter-chain contacts in protein complexes using only amino acid sequences.
  • To improve the accuracy of inter-chain contact prediction compared to state-of-the-art approaches.

Main Methods:

  • Developed ICCPred, a deep learning pipeline utilizing a deep residual network architecture.
  • Integrated a pre-trained language model with three multiple sequence alignments (MSAs) from diverse biological perspectives.
  • Trained and evaluated the model on 709 non-redundant protein complexes.

Main Results:

  • ICCPred significantly improved the accuracy of inter-chain contact prediction.
  • The method outperformed existing state-of-the-art approaches.
  • Analysis revealed that pre-trained transformer language models effectively capture co-evolutionary diversity from MSAs, enhancing prediction accuracy.

Conclusions:

  • ICCPred offers a highly accurate deep learning-based approach for predicting inter-chain contacts from protein sequences alone.
  • The method provides a valuable tool for large-scale protein-protein interaction annotation and structural biology research.