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

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 form...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Protein and Protein Structure02:15

Protein and Protein Structure

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 can...
Protein and Protein Structures02:15

Protein and Protein Structures

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 can...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

You might also read

Related Articles

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

Sort by
Same author

EC2Vec: A Machine Learning Method to Embed Enzyme Commission (EC) Numbers into Vector Representations.

Journal of chemical information and modeling·2025
Same author

A Data-Driven Approach to Enhance the Prediction of Bacteria-Metabolite Interactions in the Human Gut Microbiome Using Enzyme Encodings and Metabolite Structural Embeddings.

Nutrients·2025
Same author

Evaluating the antibacterial activity of engineered phage ФEcSw endolysin against multidrug-resistant Escherichia coli strain Sw1.

International journal of antimicrobial agents·2024
Same author

Machine Learning Techniques to Infer Protein Structure and Function from Sequences: A Comprehensive Review.

Methods in molecular biology (Clifton, N.J.)·2024
Same author

Editorial: Structure and function of trans-membrane proteins.

Frontiers in chemistry·2024
Same author

SynerGNet: A Graph Neural Network Model to Predict Anticancer Drug Synergy.

Biomolecules·2024
Same journal

Modulation of brain-kidney crosstalk by olanzapine in aluminum chloride-induced memory impairment: a preclinical investigation.

BMC research notes·2026
Same journal

Tagged and untagged amyloid precursor protein E2 domain have comparable thermal stability and metal-ion binding propensity.

BMC research notes·2026
Same journal

Phenotypical and functional characterization of a HepG2 cell clone stably overexpressing cytochrome P450 (CYP) 2C9.

BMC research notes·2026
Same journal

Inefficacy of a novel osmotic associative learning assay in C. elegans.

BMC research notes·2026
Same journal

Anticancer proteasome inhibitors are detrimental to the growth of Toxoplasma gondii in vitro.

BMC research notes·2026
Same journal

Body mass index, nutritional knowledge, and eating attitudes in dancer and non-dancer students.

BMC research notes·2026
See all related articles

Related Experiment Video

Updated: May 9, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.

Michal Brylinski1

  • 1Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. michal@brylinski.org

BMC Research Notes
|August 2, 2013
PubMed
Summary
This summary is machine-generated.

Artificial protein sequences computationally designed using eVolver enhance protein threading sensitivity. This optimization algorithm improves fold recognition for structural bioinformatics, aiding in understanding protein structure and function.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

Related Experiment Videos

Last Updated: May 9, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein engineering

Background:

  • Sequence profile-based threading is a key technique in structural bioinformatics.
  • Artificially evolved amino acid sequences can improve homology searching and protein threading sensitivity, particularly for challenging templates.

Purpose of the Study:

  • To introduce eVolver, an algorithm for computationally designing protein sequences.
  • To demonstrate the utility of evolved sequences in enhancing protein threading and fold recognition.

Main Methods:

  • Implementation details of the eVolver optimization algorithm.
  • Utilizing various potentials compatible with standard protein threading methods.
  • Case study on LARG PDZ domain using sequence profile-based fold recognition.

Main Results:

  • eVolver successfully evolves protein sequences to stabilize target structures.
  • Artificially evolved sequences show high capability in recognizing correct protein structures.
  • The evolved sequences enhance the sensitivity of standard sequence profile-based fold recognition.

Conclusions:

  • Computationally designed protein sequences can be integrated into existing threading approaches to boost sensitivity.
  • These designed sequences facilitate in silico studies on protein structure, function, and evolution.
  • eVolver is accessible as a webserver and standalone software.