DHcL specifications


Unique identifier OMICS_24454
Name DHcL
Alternative name Domain Hierarchy and closed Loops
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data A PDB identifier(s) or uploads a 3D protein structure.
Input format PDB
Output data The location of domains at different levels of hierarchy, closed loops, van der Waals locks and their interactive visualization.
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Igor Berezovsky

Publication for Domain Hierarchy and closed Loops

DHcL citations


An ambiguity principle for assigning protein structural domains

Sci Adv
PMCID: 5235333
PMID: 28097215
DOI: 10.1126/sciadv.1600552

[…] can tackle the analytical bias caused by the ambiguity of protein structure and can therefore be helpful for any field of molecular biology involving protein domain assignment. We did not mention the DHcL (Domain Hierarchy and closed Loops) method (, ), although it can compute alternative partitionings because of its low performance reported in an independent benchmarking (). We did not also menti […]


Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways

PLoS One
PMCID: 3554774
PMID: 23365638
DOI: 10.1371/journal.pone.0053642

[…] -1) RNA binding protein (PDB 2HA8) (Wu, H. et. al. unpublished data), between residues 20–88 and 89–178 (residue 20 is the first resolved residue in the crystal structure). The domain finding program DHcL also finds domains in this protein between residues 20–83 and 84–178. DHcL also finds domains in several other proteins, some generally accepted as single domain, however one of these proteins i […]

DHcL institution(s)
Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway; Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
DHcL funding source(s)
Supported by the Research Council of Norway through its allocation to the Bioinformatics Technology Platform under the functional genomics program FUGE.

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