ColBuilder is a web resource designed to generate type I collagen fibril models. ColBuilder allows to build full-atom models (structure and topology) of crosslinked collagen fibrils by integrating the low-resolution X-ray fiber diffraction with high-resolution X-ray crystallography and mass spectrometry data.
If you use ColBuilder, please cite:
https://www.biorxiv.org/content/10.1101/2024.12.10.627782v1Prior to submitting jobs to the server, users should create an account on the Register page.
After (automatic) approval of the registration, users can:
Each submitted job can be accessed in the account page. Results and logfiles are stored on the server for 14 consecutive days.
Generate Custom Triple Helix
Enable this option to create a custom triple helix structure instead of using our predefined template: type I collagen from Rattus novergicus.
Species Selection
Choose from 20 different species or provide your own FASTA sequence. This selection determines the amino acid sequence used for structure generation.
FASTA Sequences
Input area for custom FASTA sequences if not using a predefined species. Sequences should follow standard FASTA format with proper headers and sequence data as per example pre-loaded in the field.
Molecular Crosslinks
Enable this option to add molecular crosslinks to your structure. Available crosslink types and positions depend on the selected species.
N(C)-terminal Crosslink Configuration
Generate Custom Fibril Geometry
Enable this option to customize the geometric parameters of your fibril structure.
PDB Structure File
Upload a PDB format file containing the triple helix structure. Required if skipping the sequence generation step. The file should follow standard PDB format specifications and contain the following unit cell information as its first line:
CRYST1 39.970 26.950 677.900 89.24 94.59 105.58 P 1 2
Contact Distance
Determines the size of the generated fibril structure by controlling how many unit cells are included from the crystal lattice. Valid range: 15-160 Å. A larger contact distance results in a larger fibril radius, as shown in the relationship plot.
Fibril Length
Define the length of the fibril in nanometers. Valid range: 10-334 nm. This parameter determines the overall size of your fibril model.
Mix Fibrils with Different Crosslinking Patterns
Enable this option to combine fibrils with different crosslinking patterns in your model. Requires the user to already provide PDB files for two fibrils, which can be generated in the previous steps in independent runs.
First Fibril Configuration
Second Fibril Configuration
Modify Crosslink Density
Enable this option to adjust the density of crosslinks in your fibril structure. Requires the user to already provide a PDB file for a collagen fibril, which can be generated in the previous steps in independent runs.
Generate Simulation Topology Files
Enable this option to generate GROMACS topology files for molecular dynamics simulation. This requires a completed fibril structure from previous steps.
Force Field Selection
Choose the force field for molecular dynamics simulation:
The full documentation can be found on the official GitHub page of ColBuilder: https://github.com/graeter-group/colbuilder/tree/main/docs
ColBuilder is developed and maintained by the Graeter Group at the Max Planck Institute for Polymer Research.
For technical issues, bug reports, or feature requests, please submit an issue on our GitHub Issues page or email Dr. Debora Monego.
We also welcome inquiries about collaborations and scientific questions!