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

Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Networks02:26

Protein Networks

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,...

You might also read

Related Articles

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

Sort by
Same author

<i>Mycobacterium abscessus</i> bacteremia complicated by sepsis and septic shock in a patient with multiple comorbidities: a case report.

Frontiers in immunology·2026
Same author

Explainable convolutional neural network model provides an alternative genome-wide association perspective on mutations in SARS-CoV-2.

Scientific reports·2026
Same author

Genomic epidemiology and antimicrobial resistance prevalence of <i>Staphylococcus aureus</i> isolated from bloodstream infections in a tertiary hospital in central China: a 5-year retrospective study.

Frontiers in public health·2026
Same author

Privacy-preserving federated learning with optimized ensemble weighting and knowledge distillation for COVID-19 detection from non-IID medical imaging data.

Scientific reports·2026
Same author

Rapid separation of <sup>99</sup>Mo from proton irradiated thorium target for medical application.

Talanta·2026
Same author

Integrative network toxicology and single-cell transcriptomics reveal TP53 as a key mediator of PCBs-induced microglial dysfunction in diabetic retinopathy.

Ecotoxicology and environmental safety·2026
Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Asymmetric Drug-Drug Interaction Prediction Based on Generative Adversarial Networks and Knowledge Graph.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Enhancing Clinical Note Generation with ICD-10, Clinical Ontology Knowledge Graphs, and Chain-of-Thought Prompting Using GPT-4.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

<i>Special Issue:</i> 13th International Conference on Computational Advances in Bio and Medical Sciences.

Journal of computational biology : a journal of computational molecular cell biology·2026
See all related articles
  1. Home
  3. Investigations On Multiple Protein Scaffold Filling.
  1. Home
  3. Investigations On Multiple Protein Scaffold Filling.

Related Experiment Video

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Investigations on Multiple Protein Scaffold Filling.

Ismoiljon Muzaffarov1, Xiaowen Liu2, Letu Qingge3

  • 1Gianforte School of Computing, Montana State University, Bozeman, Montana, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|June 19, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

This study addresses protein scaffold filling challenges. We developed algorithms to optimize Blosum62 scores for sequence filling, with promising heuristic results for specific protein types.

Keywords:
colinear chaininggreedy algorithmslower boundprotein scaffold fillingprotein sequencingsimulated annealingtop-down and bottom-up methods

More Related Videos

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Related Experiment Videos

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Proteomics

Background:

  • Protein scaffold filling is crucial for sequence reconstruction and analysis.
  • Optimizing Blosum62 scores is key for accurate sequence alignment and comparison.

Purpose of the Study:

  • To investigate computational problems in multiple protein scaffold filling.
  • To develop algorithms for maximizing Blosum62 scores in sequence filling, with or without references.

Main Methods:

  • Theoretical analysis of algorithmic complexity, including lower bounds based on the Strong Exponential Time Hypothesis (SETH).
  • Development of a dynamic programming approach for solving the optimization problem in polynomial time for two or more scaffolds.
  • Implementation of heuristic algorithms for the specific case of three scaffolds.

Main Results:

  • A lower bound of Ω(n^(k-ε)) is established for finding k scaffolds, assuming SETH.
  • A polynomial-time dynamic programming solution is presented for the general case with two or more scaffolds.
  • Heuristic algorithms demonstrated promising empirical results on diverse protein datasets (antibody, myoglobin, etc.).

Conclusions:

  • The computational complexity of protein scaffold filling is significant, with theoretical lower bounds established.
  • Dynamic programming offers an efficient solution for multiple scaffolds, while heuristics provide practical approaches for specific cases.
  • The developed methods and heuristics show potential for applications in protein sequence analysis and reconstruction.