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Related Concept Videos

Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
Introduction to Enzymes01:22

Introduction to Enzymes

The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...
Introduction To Enzymes01:22

Introduction To Enzymes

The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...
Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
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...

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Related Experiment Video

Updated: Jul 16, 2026

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

EnzymeHunter: Achieving fine-grained enzyme function prediction with a hierarchically aware contrastive learning

Guoxin Cao1, Jian Ouyang1,2, Xiangyi Xiong1

  • 1Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.

Patterns (New York, N.Y.)
|July 15, 2026
PubMed
Summary

EnzymeHunter, a new deep learning tool, accurately predicts enzyme functions using sequence and structure. It excels at fine-grained classification and discovering novel functions, aiding biological research.

Keywords:
contrastive learningdeep learningenzyme function predictionhierarchical classificationprotein language model

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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

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Last Updated: Jul 16, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Enzymology

Background:

  • Accurate enzyme function annotation is crucial but challenging due to numerous uncharacterized proteins.
  • Distinguishing subtle functional differences between enzymes is difficult with current methods.

Purpose of the Study:

  • To develop a deep learning framework, EnzymeHunter, for fine-grained enzyme function prediction.
  • To improve the accuracy and robustness of enzyme annotation, especially for challenging cases.

Main Methods:

  • EnzymeHunter utilizes a hierarchically aware contrastive learning strategy.
  • It integrates both protein sequence and structural information.
  • The Enzyme Commission (EC) hierarchy guides the model's loss function for learning a functionally coherent embedding space.

Main Results:

  • EnzymeHunter significantly outperforms state-of-the-art models in fine-grained enzyme function prediction down to the fourth EC level.
  • The model demonstrates robust performance even in low-homology cases and accurately predicts rare enzyme classes.
  • A proteome-wide application to *Thermus thermophilus* identified novel catalytic functions, with one validated by UniProt.

Conclusions:

  • EnzymeHunter provides a powerful and accurate method for enzyme function annotation.
  • The framework's interpretability, guided by attention on critical functional sites, enhances biological understanding.
  • This tool advances the characterization of enzyme repertoires and aids in discovering new catalytic activities.