DSSP statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

DSSP specifications

Information


Unique identifier OMICS_27752
Name DSSP
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

Versioning


No version available

Publication for Define Secondary Structure of Proteins

DSSP citations

 (55)
call_split

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

2018
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 […]

call_split

Measuring evolutionary rates of proteins in a structural context

2018
F1000Res
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 […]

call_split

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

2018
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 […]

library_books

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

2017
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 […]

library_books

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

2017
Oncogenesis
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 […]

library_books

Investigating Ebola virus pathogenicity using molecular dynamics

2017
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. […]

Citations

Looking to check out a full list of citations?

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

DSSP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DSSP