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Building collagen fibrils from amino acids sequences
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graeter-group/colbuilder
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- 📋 Table of Contents
- 📚 About
- 🚀 Installation
- 🚀 Quick Start
- 📖 Usage Guide
- 📚 Documentation
- 🤝 Contributing
- 📚 Publications & Citation
- 🙏 Acknowledgements
ColBuilder is a specialized tool for generating atomistic models of collagen microfibrils from single collagen molecules. Developed by the Gräter group at the Max Planck Institute for Polymer Research, it provides researchers with a flexible framework to create biologically relevant collagen structures for molecular dynamics simulations and structural studies.
- Custom microfibril generation: Create collagen microfibrils from individual molecules or amino acid sequences with precise control over structural parameters
- Highly configurable: Adjust collagen sequence, fibril geometry, crosslink types and density to match your custom conditions
- Simulation-ready output: Generate atomistic and coarse-grained topology files compatible with major molecular dynamics packages
- Reproducible research: Standardized approach to collagen modeling to ensure consistency across studies
- Python 3.9 or later
- Git
- Conda package manager (we recommendminiforge)
Create and activate a conda environment:
conda create -n colbuilder python=3.9conda activate colbuilder
Clone the repository:
git clone git@github.com:graeter-group/colbuilder.gitcd colbuilderInstall ColBuilder:
pip install.
ColBuilder requires several external tools to function properly:
conda install conda-forge::pymol-open-source
Note: If PyMOL fails due to missinglibnetcdf.so, install:
conda install -c conda-forge libnetcdf==4.7.3
conda install muscle
- Download the latest version ofUCSF Chimera (64-bit recommended)
- Make the binary executable and run the installer:
cd~/Downloads# or wherever you downloaded the filechmod +x chimera*.bin./chimera*.bin
- Follow the installation prompts, preferably creating a symlink in a directory in your
$PATH
Note: ColBuilder specifically requires UCSF Chimera, not the newer ChimeraX.
- DownloadModeller version 10.5
- Follow the installation instructions provided
- Add the following environment variables to your
.bashrcor.bash_profile:(Adjust paths according to your installation location)export PYTHONPATH="/home/user/bin/modeller10.5/lib/x86_64-intel8/python3.3:$PYTHONPATH"export PYTHONPATH="/home/user/bin/modeller10.5/modlib:$PYTHONPATH"export LD_LIBRARY_PATH="/home/user/bin/modeller10.5/lib/x86_64-intel8:$LD_LIBRARY_PATH"
To verify your installation and run a basic example:
Verify installation:
colbuilder --help
Create a basic configuration file (save as
config.yaml):# Basic human collagen microfibril configurationspecies:"homo_sapiens"sequence_generator:truegeometry_generator:truecrosslink:truefibril_length:60.0contact_distance:20n_term_type:"HLKNL"c_term_type:"HLKNL"n_term_combination:"9.C - 947.A"c_term_combination:"1047.C - 104.C"
Run ColBuilder:
colbuilder --config_file config.yaml
The general syntax for running ColBuilder is:
colbuilder --config_file config.yaml [OPTIONS]
ColBuilder uses YAML configuration files to define parameters. Here's a complete template with all available options:
# Operation Modemode:null# Specific operation mode if neededconfig_file:null# Path to another config file (for nested configs)sequence_generator:true# Generate sequence from speciesgeometry_generator:true# Generate fibril geometrytopology_generator:false# Generate topology filesdebug:false# Enable debug modeworking_directory:"./"# Working directory for inputs/outputs# Input Configurationspecies:"homo_sapiens"# Species for collagen sequence# Available species options:# Mammals (Primates): homo_sapiens, pan_troglodytes, pongo_abelii, callithrix_jacchus, otolemur_garnettii# Mammals (Rodents): mus_musculus, rattus_norvegicus# Mammals (Other): bos_taurus, canis_lupus, ailuropoda_melanoleuca, mustela_putorius, myotis_lucifugus, loxodonta_africana# Fish: danio_rerio, oreochromis_niloticus, oryzias_latipes, tetraodon_nigroviridis, xiphophorus_maculatus# Reptiles: pelodiscus_sinensis# Sequence Settingsfasta_file:null# Custom FASTA file path (if null, auto-generated based on species)crosslink:true# Enable crosslinking in the modeln_term_type:"HLKNL"# N-terminal crosslink type (Options: "DPD", "DPL", "HLKNL", "LKNL", "PYD", "PYL", "deHHLNL", "deHLNL", "NONE")c_term_type:"HLKNL"# C-terminal crosslink type (Options: "DPD", "DPL", "HLKNL", "LKNL", "PYD", "PYL", "deHHLNL", "deHLNL", "NONE")n_term_combination:"9.C - 947.A"# N-terminal residue combinationc_term_combination:"1047.C - 104.C"# C-terminal residue combination# Geometry Parameterspdb_file:null# Input PDB file (set to null if sequence_generator is true)contact_distance:20# Distance threshold for contacts (Å)fibril_length:70.0# Length of the generated fibril (nm)crystalcontacts_file:null# File with crystal contactsconnect_file:null# File with connection informationcrystalcontacts_optimize:false# Optimize crystal contacts during generation# Mixing Options (for mixed crosslinked microfibril)mix_bool:false# Enable mixing of different crosslink typesratio_mix:"A:70 B:30"# Format: "Type:percentage Type:percentage"files_mix:# Required if mix_bool is true -"collagen-molecule-crosslinkA.pdb"# PDB file of collagen molecule with type A crosslinks -"collagen-molecule-crosslinkB.pdb"# PDB file of collagen molecule with type B crosslinks# Replacement Options (for fewer crosslinks)replace_bool:false# Enable crosslink replacementratio_replace:30# Percentage of crosslinks to replacereplace_file:null# File with crosslinks to be replaced (set to null if geometry_generation is true)# Topology Optionsforce_field:"amber99"# Force field for topology generation (Options: "amber99", "martini3")
For a complete list of configuration options, see thedetailed documentation.
# config_human_basic.yamlspecies:"homo_sapiens"sequence_generator:truegeometry_generator:truecrosslink:falsefibril_length:40.0contact_distance:25
colbuilder --config_file config_human_basic.yaml
# config_bovine_crosslinked.yamlspecies:"bos_taurus"sequence_generator:truegeometry_generator:truecrosslink:truen_term_type:"HLKNL"c_term_type:"HLKNL"n_term_combination:"9.C - 946.A"c_term_combination:"1046.C - 103.C"fibril_length:80.0contact_distance:15
colbuilder --config_file config_bovine_crosslinked.yaml
# config_mixed_crosslinks.yamlspecies:"homo_sapiens"sequence_generator:falsegeometry_generator:falsemix_bool:trueratio_mix:"D:80 T:20"files_mix: -"human-D.pdb" -"human-T.pdb"
colbuilder --config_file config_mixed_crosslinks.yaml
# config_topology.yamlspecies:"homo_sapiens"sequence_generator:false`geometry_generator:truetopology_generator:truepdb_file:"path/to/template_collagen_molecule.pdb"force_field:"martini3"
colbuilder --config_file config_topology.yaml
For detailed API documentation, advanced usage examples, and theoretical background:
We welcome contributions to ColBuilder! Please see ourcontributing guidelines for details on how to submit issues, pull requests, and code reviews.
If you use ColBuilder in your research, please cite our paper:
https://www.biorxiv.org/content/10.1101/2024.12.10.627782v1
A BibTeX entry is provided in theCITATION.cff file.
ColBuilder is developed and maintained by the Gräter group at the Max Planck Institute for Polymer Research. We thank all contributors that have supported this work.
For questions, feedback, or support, pleaseopen an issue on our GitHub repository.
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Building collagen fibrils from amino acids sequences