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ColBuilder: Flexible structure generation of crosslinked collagen fibrils
Open accessPreprint — published as 10.1093/bioinformatics/btaf278
Abstract
Collagen 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. ColBuilder 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 335 nm-long fibrils validate the generated structures, showing excellent agreement with experimental measurements of D-band periodicity and force-extension behavior. ColBuilder is available both as an open-source command-line application and through a web interface at colbuilder.mpip-mainz.mpg.de.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Flagged first, then by citations
Research works printed but not linked: 41
- 10.1042/bj3160001 · DOI
- 10.1146/annurev.biochem.77.032207.120833 · DOI · Paper page
- 10.1073/pnas.0502718103 · DOI · Paper page
- 10.1038/284531a0 · DOI
- 10.1074/jbc.M112.390146 · DOI
- 10.1021/jp1059984 · DOI
- 10.1021/jp0440941 · DOI
- 10.1016/j.jmbbm.2014.07.008 · DOI
- 10.1038/s41467-020-15567-4 · DOI
- 10.1073/pnas.0710588105 · DOI
- 10.1039/c0sm01192d · DOI
- 2018, Charmm-gui membrane builder for complex biological membrane simulations with glycolipids and lipoglycans, Journal of chemical theory and computation, 15, 775
- 10.1002/jcc.21224 · DOI
- 10.1002/jcc.25773 · DOI
- 10.1016/J.BPJ.2021.07.009 · DOI
- 10.1093/bioinformatics/btp163 · DOI · Paper page
- 10.1093/nar/gkh340 · DOI · Paper page
- 10.1126/science.7695699 · DOI
- Eric F. Pettersen , Thomas D. Goddard , Conrad C. Huang , Gregory S. Couch , Daniel M. Greenblatt , Elaine C. Meng , and Thomas E. Ferrin . UCSF Chimera—A visualization system for exploratory research and analysis. 25(13):1605–1612. · DOI
- Dennis W. Bennett . Understanding Single-Crystal X-ray Crystallography. Wiley-VCH-Verl, 2010.
- J Macqueen . Some methods for classification and analysis of multivariate observations. In Proceedings of 5-th Berkeley Symposium on Mathematical Statistics and Probability/University of California Press, 1967.
- 2011, Scikit-learn: Machine learning in python, the Journal of machine Learning research, 12, 2825
- 10.1016/S0006-3495(93)81362-6 · DOI
- 10.11138/mltj/2014.4.3.303 · DOI
- 2016, Tensile mechanical properties of collagen type i and its enzymatic crosslinks, Biophysical chemistry, 214, 1
- 10.1038/s41467-023-37726-z · DOI
- 10.2337/diab.45.3.S67 · DOI
- 2014, The role of collagen crosslinks in ageing and diabetes-the good, the bad, and the ugly, Muscles, ligaments and tendons journal, 4, 303
- 10.1002/jcc.20291 · DOI
- 10.1021/jp901540t · DOI
- 10.1002/prot.22711 · DOI
- Jaewoon Jung , Kiyoshi Yagi , Cheng Tan , Hiraku Oshima , Takaharu Mori , Isseki Yu , Yasuhiro Matsunaga , Chigusa Kobayashi , Shingo Ito , Diego Ugarte La Torre , et al. Genesis 2.1: High-performance molecular dynamics software for enhanced sampling and free-energy calculations for atomistic, coarse-grained, and quantum mechanics/molecular mechanics models. The Journal of Physical Chemistry B, 2024. · DOI
- 10.1002/jcc.26450 · DOI
- 2007, Accurate sampling using langevin dynamics, Physical review E-Statistical, Nonlinear, and Soft Matter Physics, 75, 056707, 10.1103/PhysRevE.75.056707 · DOI
- 10.1063/1.467468 · DOI
- 2018, Optimal temperature evaluation in molecular dynamics simulations with a large time step, Journal of Chemical Theory and Computation, 15, 84
- Jaewoon Jung and Yuji Sugita . Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step. The Journal of Chemical Physics, 153(23), 2020. · DOI
- 10.1016/0021-9290(90)90038-5 · DOI
- 10.1039/C9NR02644D · DOI
- 10.1016/j.bpj.2020.01.038 · DOI
- 10.1021/bm900519v · DOI
Metadata
- Authors
- Monego, D., Brosz, M., Buck, J., Viliuga, V., Jung, J., Stuehn, T., Schmies, M., Sugita, Y., & Gräter, F.
- Affiliations
- Max Planck Institute for Polymer Research (DE)
- Heidelberg University (DE)
- Stockholm University (SE)
- RIKEN Center for Computational Science (JP)
- Corresponding author
- Monego, Debora
- Gräter, Frauke
- ORCID
- Venue
- Bioinformatics
- Publisher
- openRxiv
- Published
- 2024-12-12
- Volume
- 41
- Issue
- 6
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC12148304
- OpenAlex
- W4410079575
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 2 · 2025: 2
- FWCI
- 0.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- Funders
- Deutsche Forschungsgemeinschaft (EXC-2082/ 1390761711, 390761711, 2082/1, 2082/1390761711, EXC-2082/1)
- Klaus Tschira Stiftung
- RIKEN (hp230212)
- H2020 European Research Council (101002812)
- Topics
- Physical Sciences › Materials Science › Biomaterials › Collagen: Extraction and Characterization
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Connective tissue disorders research
- Keywords
- collagen fibrils, crosslinking, homology modeling, higher-order structure, force-extension behavior, connective tissue
- MeSH terms
- Collagen, Cross-Linking Reagents, Protein Conformation, Software, Molecular Dynamics Simulation
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