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Related Concept Videos

Fibril-associated Collagen01:11

Fibril-associated Collagen

Fibril-associated collagens are a type of collagens present in the extracellular matrix with interrupted triple helices or FACIT (Fibril-associated collagens interrupted triple-helices). FACIT help connect and attach the collagen fibrils with each other as well as with other proteins of the extracellular matrix.
For example, the type II collagen fibrils in cartilage have covalently bound type IX fibril-associated collagens at regular intervals. Other types of fibril-associated collagens are...
Type IV Collagen of Basal Lamina01:05

Type IV Collagen of Basal Lamina

Type IV collagen is a 400 nm long, network-forming collagen that acts as a barrier between the epithelial and endothelial cells. Type IV collagen  forms the backbone of the basement membrane by scaffolding with laminin, entactin, proteoglycans, and fibronectin. Apart from rendering structural support to the basement membrane, it also helps entail signaling potentials necessary for both pathological and physiological functions.
A type IV collagen molecule has six alpha chains which can exist in...
Classification of Connective Tissues01:30

Classification of Connective Tissues

The connective tissues have different properties and functions in the human body. They are broadly categorized into proper, supporting, or fluid connective tissues.
Connective Tissue Proper
Connective tissue proper is the most abundant class of connective tissues. As its name implies, it predominantly connects different tissues in the body. Depending on the cell types, ground substance, viscosity, and fiber types in the ECM, connective tissue proper is further categorized into loose and dense.
Collagens are the Major Structural Proteins of ECM01:13

Collagens are the Major Structural Proteins of ECM

Three main types of fibers are secreted by fibroblasts: collagen fibers, elastic fibers, and reticular fibers. Collagen fiber is made from fibrous protein subunits linked together to form a long, straight fiber. Collagen fibers, while flexible, have great tensile strength, resist stretching, and give ligaments and tendons their characteristic resilience and strength. These fibers hold connective tissues together, even during the body's movement.
Connective tissue proper includes loose...
Fibrous Proteins00:55

Fibrous Proteins

Fibrous proteins are either long and narrow proteins or assemble to form long and thin structures. They contain repetitive units and usually consist of either alpha helices or beta sheets and, in rare cases, a mix of both. The amino acids in the primary structure often consist of repeating amino acid sequences. The role of fibrous proteins is primarily structural. Many are located in the extracellular matrix and are present in connective tissues to impart strength and joint mobility. They are...
Classification of Skeletal Muscle Fibers01:48

Classification of Skeletal Muscle Fibers

Skeletal muscles continuously produce ATP to provide the energy that enables muscle contractions. Skeletal muscle fibers can be categorized into three types based on differences in their contraction speed and how they produce ATP, as well as physical differences related to these factors. Most human muscles contain all three muscle fiber types, albeit in varying proportions.
Slow-Twitch Muscle Fibers
Slow oxidative, muscle fibers appear red due to large numbers of capillaries and high levels of...

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Updated: Jun 23, 2026

Unilateral Lung Volume Analysis Using Micro-CT for Enhanced Assessment of Pulmonary Fibrosis in Preclinical Models
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Published on: June 20, 2025

Predict collagen hydroxyproline sites using support vector machines.

Zheng Rong Yang1

  • 1School of Biosciences, University of Exeter, Exeter, United Kingdom. z.r.yang@ex.ac.uk

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|May 13, 2009
PubMed
Summary
This summary is machine-generated.

Researchers developed predictive models for collagen hydroxyproline sites, crucial for understanding disease and signaling. The best model achieved 90% sensitivity and 70% specificity in predictions.

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Production of Nanofibrillar Patterned Collagen for Tissue Engineering
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Production of Nanofibrillar Patterned Collagen for Tissue Engineering

Published on: September 20, 2024

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Collagen hydroxyproline is a key posttranslational modification linked to various diseases and cellular signaling pathways.
  • Predicting collagen hydroxyproline sites is essential for biological and medical research, yet no predictive models currently exist.

Purpose of the Study:

  • To develop and evaluate computational models for accurately predicting collagen hydroxyproline sites.
  • To establish a foundation for future research into the roles of collagen hydroxyproline in health and disease.

Main Methods:

  • Utilized support vector machines (SVMs) with identity and bio-kernel functions for model construction.
  • Generated peptide data from 37 NCBI-sourced collagen sequences using a sliding window approach.
  • Employed fivefold cross-validation for rigorous model performance assessment.

Main Results:

  • The developed SVM models demonstrated predictive capabilities for collagen hydroxyproline sites.
  • The optimal model achieved a high sensitivity of 90% and a specificity of 70%.

Conclusions:

  • The study successfully constructed predictive models for collagen hydroxyproline sites using SVMs.
  • These models represent a significant advancement in the computational prediction of posttranslational modifications in collagen.