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Related Concept Videos

Protein Families02:47

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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 locations, protein...
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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,...
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Related Experiment Video

Updated: Jun 13, 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

PathPred: an enzyme-catalyzed metabolic pathway prediction server.

Yuki Moriya1, Daichi Shigemizu, Masahiro Hattori

  • 1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

Nucleic Acids Research
|May 4, 2010
PubMed
Summary

PathPred is a web server that predicts multi-step reaction pathways using biochemical transformation patterns from the KEGG RPAIR database. It aids in understanding microbial biodegradation and plant metabolite biosynthesis.

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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

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Last Updated: Jun 13, 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

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Metabolic Engineering

Background:

  • The KEGG RPAIR database compiles biochemical transformation patterns (RDM patterns) and chemical structure alignments for enzyme-catalyzed reactions.
  • Understanding complex metabolic pathways is crucial for fields like biodegradation and biosynthesis.

Purpose of the Study:

  • To introduce PathPred, a web-based server for predicting multi-step reaction pathways.
  • To focus pathway prediction on microbial biodegradation and plant secondary metabolite biosynthesis.

Main Methods:

  • Utilizing the KEGG RPAIR database's RDM patterns and reactant pair library.
  • Employing local RDM pattern matching and global chemical structure alignment for prediction.
  • Developing a web server accessible at http://www.genome.jp/tools/pathpred/.

Main Results:

  • PathPred successfully predicts plausible multi-step reaction pathways.
  • The server focuses on 947 RDM patterns for biodegradation and 1397 for biosynthesis.
  • Predicted pathways are visualized as tree-shaped graphs, including transformed compounds and reference patterns.

Conclusions:

  • PathPred offers a valuable tool for exploring biochemical pathways.
  • The server facilitates research in microbial biodegradation and plant metabolite biosynthesis.
  • The approach leverages comprehensive biochemical data for pathway prediction.