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Resource:Database of Secondary Structure Assignments

Name: Resource:Database of Secondary Structure Assignments
Description: Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries.

DSSP is distributed on a basis of trust and instructions are available on the site.

  • Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead:

dsspcmbi source.pdb destination.dssp > messages.txt

  • Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code.
  • FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.
Abbreviation: DSSP
Parent Organization: Radboud University Nijmegen; Nijmegen; Netherlands
Resource Type(s): Web accessible database, Downloadable database, Software resource
Resource: Resource
URL: http://swift.cmbi.ru.nl/gv/dssp/
*Id: nif-0000-23901
PMID: PMID 6667333, 21071423
Publication link: http://nar.oxfordjournals.org/content/39/suppl_1/D411.long
Availability: Free. If you use DSSP, please cite. DSSP 2.8 is provided under the Boost Software License.
Address: CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA NIJMEGEN, The Netherlands
Keywords: Amino Acid Sequence, Hydrogen Bonding, Protein Conformation, Proteins, Gold standard or authority
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

This resource will be curated within 7 days.

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Notes

This page uses this default form:Resource

Alt. URL for mirror: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+DSSP
Old URL: http://www.sander.ebi.ac.uk/dssp/

Contributors

Aarnaud, Ccdbuser, Nifbot2, Zaidaziz



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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:Database of Secondary Structure AssignmentsRDF feed
AbbrevDSSP  +
AddressCMBI  +, NCMLS  +, Radboud University Nijmegen Medical Centre  +, Geert Grooteplein 26-28  +, 6525 GA NIJMEGEN  +, and The Netherlands  +
AltURLhttp://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page%2BLibInfo%2B-lib%2BDSSP  +
AvailabilityFree. If you use DSSP  +, and Please cite. DSSP 2.8 is provided under the Boost Software License.  +
CurationStatuscurated  +
DefiningCitationhttp://swift.cmbi.ru.nl/gv/dssp/  +
DefinitionDatabase of secondary structure assignment Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries.

DSSP is distributed on a basis of trust and instructions are available on the site.

  • Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead:

dsspcmbi source.pdb destination.dssp > messages.txt

  • Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code.
  • FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.
    d DSSP files with the rsync command.
ExampleImageDSSP.PNG  +
Has default formThis property is a special property in this wiki.Resource  +
Has roleSoftware resource  +, and Database  +
Idnif-0000-23901  +
Is part ofRadboud University Nijmegen; Nijmegen; Netherlands  +
KeywordsAmino Acid Sequence  +, Hydrogen Bonding  +, Protein Conformation  +, Proteins  +, and Gold standard  +
LabelResource:Database of Secondary Structure Assignments  +
ModifiedDate4 August 2014  +
OldURLhttp://www.sander.ebi.ac.uk/dssp/  +
PMID6667333, 21071423  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://nar.oxfordjournals.org/content/39/suppl_1/D411.long  +
SuperCategoryResource  +