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Related Concept Videos

Energy Diagrams, Transition States, and Intermediates02:13

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Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
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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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Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
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Rate laws describe the relationship between the rate of a chemical reaction and the concentration of its reactants. In a rate law, the rate constant k and the reaction orders are determined experimentally by observing how the rate of reaction changes as the concentrations of the reactants are changed. A common experimental approach to the determination of rate laws is the method of initial rates. This method involves measuring reaction rates for multiple experimental trials carried out using...
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Updated: Jul 12, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference.

Spencer Krieger1, John Kececioglu2

  • 1Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 31, 2023
PubMed
Summary
This summary is machine-generated.

We developed Mmunin, a new tool that provides the first cutting-plane algorithm for modeling shortest hyperpaths in cellular biology. This algorithm accurately models complex reaction networks in signaling and metabolic pathways.

Keywords:
cell signaling networkscombinatorial optimizationcutting plane algorithmsdirected hypergraphsinferring pathwaysinteger linear programmingmetabolic networksshortest hyperpathssystems biology

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Area of Science:

  • Cellular biology
  • Systems biology
  • Biochemistry

Background:

  • Signaling and metabolic pathways are fundamental to cellular biology, involving complex reaction networks.
  • Accurate modeling of these pathways is crucial for understanding cellular functions.

Purpose of the Study:

  • To introduce a novel algorithm for modeling shortest hyperpaths in biological pathways.
  • To provide a computational tool for analyzing complex reaction networks.

Main Methods:

  • Development of a cutting-plane algorithm specifically designed for shortest hyperpath problems.
  • Implementation of the algorithm in a publicly available software tool named Mmunin.

Main Results:

  • The study presents the first cutting-plane algorithm for shortest hyperpaths.
  • The Mmunin tool offers a practical solution for modeling biological reaction networks.

Conclusions:

  • The developed algorithm and Mmunin tool advance the capability to model and analyze biological pathways.
  • This work provides a valuable resource for researchers in cellular and systems biology.