ColBuilder is a web resource of type I collagen fibril models.
We provide fibril models for 21 species with different crosslink types observed in collagen. Users can choose from the divalent crosslinks:
- HLKNL (hydroxylysino‐keto‐norleucine)
- LKNL (lysino-keto-norleucine)
- deH‐HLNL (dehydro-hydroxylysino-norleucine)
- deH-LNL (dehydro-lysino-norleucine)
or trivalent crosslinks:
- PYD (pyridinoline),
- DPD (deoxy-pyridinoline)
- PYL (pyrrole)
- DPL (deoxy-pyrrole)
Pairs of crosslinked lysine residues are not unambiguously defined, therefore we constructed models for all possible pairs of lysine residues that were properly positioned for the crosslink formation e.g. for Homo sapiens:
We also provide force-field parameters that can be used for atomistic MD simulations.
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