ColBuilder: A server to build collagen fibril models.


Type I collagen is the main structural component of many tissues in the human body. It provides excellent mechanical properties to connective tissue and acts as a protein interaction hub. There is thus a wide interest in understanding the properties and diverse functions of type I collagen at the molecular level. A precondition is an atomistic collagen I structure as it occurs in native tissue. To this end, we built full-atom models of cross-linked collagen fibrils by integrating the low-resolution structure of collagen fibril available from x-ray fiber diffraction with high-resolution structures of short collagen-like peptides from x-ray crystallography and mass spectrometry data. We created a Web resource of collagen models for 20 different species with a large variety of cross-link types and localization within the fibril to facilitate structure-based analyses and simulations of type I collagen in health and disease. To easily enable simulations, we provide parameters of the modeled cross-links for an Amber force field. The repository of collagen models is available at


PubMed ID: 34265261

DOI: 10.1016/j.bpj.2021.07.009

Research Groups: Molecular Biomechanics

Publication type: Journal

Journal: Biophysical Journal

Citation: Biophysical Journal,120(17):3544-3549

Date Published: 7th Sep 2021


Registered Mode: manually

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Obarska-Kosinska, A., Rennekamp, B., Ünal, A., & Gräter, F. (2021). ColBuilder: A server to build collagen fibril models. In Biophysical Journal (Vol. 120, Issue 17, pp. 3544–3549). Elsevier BV.

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Created: 27th Oct 2021 at 05:41

Last updated: 5th Mar 2024 at 21:24

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