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DSSPcont specifications

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Unique identifier OMICS_19955
Name DSSPcont
Interface Web user interface
Restrictions to use None
Input data A protein.
Computer skills Basic
Stability No
Maintained No

Publication for DSSPcont

DSSPcont citations

 (6)
library_books

Characterization of long and stable de novo single alpha helix domains provides novel insight into their stability

2017
PMCID: 5347031
PMID: 28287151
DOI: 10.1038/srep44341

[…] myosin-6 and its k-only and r-only mutants (m6wt, m6k, m6r)., wordom was used to analyse the simulation trajectories. the secondary structure of the protein was assigned for each timeframe using the dsspcont criteria. this was then used to calculate the helicity (or average helical fraction) of the protein overall. for the salt bridge analysis, the distance between lys nζ and the centroid […]

library_books

Computational Prediction of RNA Binding Proteins and Binding Sites

2015
PMCID: 4661811
PMID: 26540053
DOI: 10.3390/ijms161125952

[…] (ss) provides local and geometric patterns, which can be obtained in two ways: one is that the protein structure is available and real ss could be calculated using ss assignment approach such as dsspcont [,], the other is that the protein structure is unavailable and predicted ss could be obtained using ss predicted algorithm such as psipred [,,]. ss has been employed as an encoding feature […]

library_books

An Overview of the Prediction of Protein DNA Binding Sites

2015
PMCID: 4394471
PMID: 25756377
DOI: 10.3390/ijms16035194

[…] prediction methods [,] (e.g., psipred []); for a structural-based prediction, the sss can be calculated from the corresponding structure through secondary structure assignment methods [] (e.g., dsspcont []). several studies have employed the sss of a residue as the encoding information in the prediction of dna–binding residues. note that the secondary structure was not considered […]

library_books

Stable Single α Helices Are Constant Force Springs in Proteins*

2014
PMCID: 4183817
PMID: 25122759
DOI: 10.1074/jbc.M114.585679

[…] and c-terminal carbonyl carbon atom (rnc)) of at least 8 nm had been reached. wordom (version 21) was used to analyze the simulation trajectories (, ). helicity values were calculated using wordom “dsspcont” assignments of residue secondary structure., the aim of the experiments reported here was to test the force-extension properties of a sah domain. we chose to use the putative sah domain […]

library_books

Iterative Structure Based Peptide Like Inhibitor Design against the Botulinum Neurotoxin Serotype A

2010
PMCID: 2894858
PMID: 20614028
DOI: 10.1371/journal.pone.0011378

[…] s: bend)., α: helical chirality (dihedral α angle – positive angle corresponds to a right-handed helix)., rrgx: any of the tetrapeptides reported in ., all ss and α values were calculated with the dsspcont program dsspcont: continuous secondary structure assignments for proteins ., a helical backbone conformation is also observed in the zn-chelating cratkml plm, similarly encompassing […]

library_books

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures

2006
PMCID: 1386714
PMID: 16478545
DOI: 10.1186/1471-2105-7-68

[…] solution of a protein structure always provides a number of models with structural variation due, at least in part, to intrinsic motions of the protein []. andersen and colleagues developed a scheme-dsspcont-where the secondary state probability distribution for each residue in a protein is estimated from the variation amongst an ensemble of nmr models of the protein. the dsspcont assignment […]


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DSSPcont institution(s)
CUBIC, Department of Biochemistry and Molecular Biophysics and 2 North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; BASF AG, Ludwigshafen, Germany; Structural Bioinformatics Group, Department of Biological Sciences, Imperial College, London, UK; Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, New York, NY, USA
DSSPcont funding source(s)
Supported by the grants 1-P50- GM62413-01 and RO1-GM63029-01 from the National Institute of Health (NIH).

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