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DSSP specifications


Unique identifier OMICS_27752
Alternative name Define Secondary Structure of Proteins
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 3.0.0
Stability Stable
Maintained Yes


No version available

Publication for Define Secondary Structure of Proteins

DSSP citations


Hsp90 shapes protein and RNA evolution to balance trade offs between protein stability and aggregation

Nat Commun
PMCID: 5934419
PMID: 29725062
DOI: 10.1038/s41467-018-04203-x
call_split See protocol

[…] n-prone; and as hydrophobic if ΔHyd > 4, and otherwise non-hydrophobic else (Extended Data Fig. ). Solvent accessible surface area (ASA) for each residue was computed from the PDB structures with the DSSP program,. Residues were considered buried with ASA < 30, at the interface if the residue contributes ASA > 30 to the monomer interface in the assembled capsid, and as surface residue if ASA > 50 […]


Measuring evolutionary rates of proteins in a structural context

PMCID: 5676193
PMID: 29167739
DOI: 10.5256/f1000research.13954.r27048
call_split See protocol

[…] SPmkDSSP is a tool that calculates solvent accessibilities and parses secondary structure assignments from a PDB input file into a standardized format . This format follows that of the entries in the DSSP database . Download the mkDSSP software from https://slackbuilds.org/repository/14.2/academic/mkDSSP/.PythonDownload python from https://www.python.org/downloads/.BiopythonBiopython is a python l […]


Role of N glycosylation in activation of proMMP 9. A molecular dynamics simulations study

PLoS One
PMCID: 5766141
PMID: 29329315
DOI: 10.1371/journal.pone.0191157
call_split See protocol

[…] of the trajectory frames and to strip water and counter ions from the trajectory for visualization with VMD. The root means square deviation (RMSD), root mean square fluctuation (RMSF), B-factor, and dssp modules were used to analyze each frame of the MD production runs to determine the average overall fluctuation, conformational fluctuation of each residue and secondary structure. The solvent-acc […]


The Cryoelectron Microscopy Structure of the Type 1 Chaperone Usher Pilus Rod

PMCID: 5719983
PMID: 29129382
DOI: 10.1016/j.str.2017.10.004

[…] structure from previous NMR and crystallography studies were used to guide building and refinement (, , ). However, in order to obtain an unbiased view of secondary structure element boundaries, the DSSP server (, ) was used in combination with careful manual examination of the model in Coot to delineate the final secondary structure element boundaries enforced during real space refinement. Final […]


Spatial distribution of disease associated variants in three dimensional structures of protein complexes

PMCID: 5623905
PMID: 28945216
DOI: 10.1038/oncsis.2017.79

[…] served for nsSNVs mapped into resolved 3D structures.When analyzing the distribution of the corresponding positions in the template structures with respect to the elements of secondary structure with DSSP using a majority vote over all available template structures, we find no significant trends related to pathogenicity of the corresponding sets: overall, between 32.5 and 43.1% of positions corres […]


Investigating Ebola virus pathogenicity using molecular dynamics

BMC Genomics
PMCID: 5558184
PMID: 28812539
DOI: 10.1186/s12864-017-3912-2

[…] all the trajectories. Rotational and translational movements were then deleted in order to perform the Principal Component Analysis. Secondary structure plots for trajectories were obtained using the DSSP [] tool in gromacs. Root mean square deviation (RMSD) and fluctuation (RMSF) from the initial starting complex were obtained using Bio3D, as well as the PCA analysis and correlation plots. […]


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DSSP institution(s)
Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; Netherlands Bioinformatics Centre, Nijmegen, The Netherlands; European Molecular Biology Laboratory – Heidelberg, Heidelberg, Germany; Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

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