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Related Concept Videos

Protein Networks02:26

Protein Networks

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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,...
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Protein Networks02:26

Protein Networks

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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Protein Organization01:24

Protein Organization

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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....
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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...
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Related Experiment Video

Updated: Jan 9, 2026

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

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Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence-function relationships

Yueming Long1, Fatemeh Abbasinejad2, Francesca-Zhoufan Li3

  • 1Division of Chemistry and Chemical Engineering, California Institute of Technology, California Blvd., Pasadena, CA 91125, United States.

Nucleic Acids Research
|December 8, 2025
PubMed
Summary
This summary is machine-generated.

A new Enzyme Engineering Database centralizes enzyme sequence-function data. This resource aids machine learning-guided enzyme engineering by providing data and analysis tools for researchers.

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Area of Science:

  • Biotechnology and bioengineering
  • Enzyme discovery and engineering
  • Bioeconomy applications

Background:

  • Enzyme engineering is crucial for the bioeconomy, but lacks sufficient data for machine learning approaches.
  • Existing resources do not adequately capture or interpret enzyme engineering datasets.
  • A need exists for centralized data repositories and analysis tools in enzyme engineering.

Purpose of the Study:

  • To establish a centralized database for enzyme engineering sequence-function data.
  • To provide online analysis and visualization tools for protein engineers.
  • To create a benchmark dataset and extraction pipeline for machine learning in enzyme engineering.

Main Methods:

  • Development of the Enzyme Engineering Database (EEDb) as a public data repository.
  • Implementation of online tools for data analysis and visualization of enzyme variants.
  • Creation of a gold-standard dataset and a large language model (LLM) pipeline for automated data extraction.

Main Results:

  • The EEDb provides a centralized platform for depositing and accessing enzyme engineering data.
  • Integrated tools enable researchers to analyze their data and compare enzyme variants.
  • A specialized LLM extraction pipeline and benchmark dataset were developed for enzyme engineering campaigns.

Conclusions:

  • The Enzyme Engineering Database addresses the critical need for data and tools in enzyme engineering.
  • This resource facilitates machine learning-guided enzyme discovery and optimization.
  • The EEDb promotes data sharing and advances the field of protein engineering.