ArticleBioinformatics (Oxford, England)2025
ColBuilder: flexible structure generation of crosslinked collagen fibrils.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 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
4 citing papers in PubMed.
- 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
- Coarse-grained Martini 3 model for collagen fibrils.Biophysical journal · 2026Article
- Evaluation and refinement of all-atom force fields for reproducing collagen structure and dynamics.Biophysical journal · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
motivationCollagen fibrils are fundamental building blocks of connective tissues, yet generating accurate molecular models of their structure remains challenging due to their hierarchical organization and complex crosslinking patterns.
resultsColBuilder has been developed to automate the generation of atomistic models of crosslinked collagen fibrils and facilitate the setup of molecular simulations. The tool integrates homology modeling, higher order structure generation and optimization to build complete fibril structures with precise control over sequence composition, crosslinking patterns, and dimensions. Users can explore different collagen sequences, manipulate crosslink chemistry through mixed ratios and densities, and generate fibrils of varying diameter and length. All-atom molecular dynamics simulations of 335nm-long fibrils validate the generated structures, showing excellent agreement with experimental measurements of D-band periodicity and force-extension behavior. AVAILABILITY AND IMPLEMENTATION: ColBuilder is available both as an open-source command-line application and through a web interface at https://colbuilder.mpip-mainz.mpg.de.
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What Socratic holds
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 Socratic graph.