ArticleBiophysical journal2021
ColBuilder: A server to build collagen fibril models.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 30 citations in OpenAlex.
- Article
- Free energy of collagen-mimetic peptide dimerization and implications for fibrillization.Biophysical journal · 2026Article
- Introducing non-enzymatic crosslinks into atomistic simulations of collagen fibrils.Bioinformatics (Oxford, England) · 2026Article
- Synthetic Surrogates of Collagen-Rich Microenvironments: Integrating Modular Bioactive Fibrillar Structure and Tunable Viscoelasticity via Multifunctional Assembling Peptides.ACS central science · 2026Article
- Learning potential energy surfaces of hydrogen atom transfer reactions in peptides.Digital discovery · 2026Article
- Supramolecular Assembly of Collagen-Mimetic Peptide D-Periodic Fibrils and Nanoassemblies.Biomacromolecules · 2026Article
- Evaluation and refinement of all-atom force fields for reproducing collagen structure and dynamics.Biophysical journal · 2025Article
- ColBuilder: flexible structure generation of crosslinked collagen fibrils.Bioinformatics (Oxford, England) · 2025Article
- Deciphering the folding code of collagens.Nature communications · 2025Article
- Revealing the Solution Conformation and Hydration Structure of Type I Tropocollagen Using X-ray Scattering and Molecular Dynamics Simulation.Biomacromolecules · 2025Article
- Review
- Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins.Chemical science · 2024Article
- Collagen breaks at weak sacrificial bonds taming its mechanoradicals.Nature communications · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 https://colbuilder.h-its.org.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.