PSSMSearch is a web application to discover novel protein motifs (SLiMs, mORFs, miniMotifs) and PTM sites. PSSMSearch analyses proteomes for regions with significant similarity to a specificity determinant model built from a set of aligned functional peptides. Query peptides can be provided by the users or retrieved from the ELM database. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the specificity determinant model and users can modify the model to add prior knowledge of specificity determinants through an interactive PSSM heatmap.


If you use PSSMSearch for your research, please cite the most recent publication:

"PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants" Izabella Krystkowiak, Jean Manguy, Norman E Davey; Nucleic Acids Research, gky426 doi:10.1093/nar/gky426


PSSMSearch licence and code

PSSMSearch is available for download and use under a GNU General Public License. It allows the users (individuals, organizations, companies) to run, study, share (copy), and modify the software. However, it requires that when distributing derived works, the source code of the work must be made available under the same license.

For the full license please see GNU GPL v3 licence.

End-user licence agreement

  1. The developers of PSSMSearch require attribution for its service.
  2. Any use of the PSSMSearch is non-confidential.
  3. Users of PSSMSearch agree not to attempt to use any part of the UCD computers, files or networks apart from through the service interfaces provided.
  4. The developers of PSSMSearch do not guarantee the accuracy of any data contained herein, nor the suitability of the PSSMSearch web service for any purpose.
  5. If any single user exploits the PSSMSearch web service to a level that prevents, or looks set to prevent, the developers of PSSMSearch providing services to others, the developers of PSSMSearch may discontinue service to that user. The developers of PSSMSearch will then contact the user to discuss their needs and how (and if) these can be met.
  6. For planning and scientific review purposes, the developers of PSSMSearch will keep records of usage. Logs of usage may also be maintained for the purposes of monitoring and improving services, and measuring the impact a particular service has on our resources.
  7. The developers of PSSMSearch will make reasonable effort to maintain continuity of service and provide adequate warning of any changes or discontinuities. However, the developers of PSSMSearch accepts no responsibility for the consequences of any temporary or permanent discontinuity in service.
  8. The developers of PSSMSearch itself places no restrictions on the use or redistribution of the data available via the PSSMSearch service. However, the original data may be subject to patent, copyright, or other intellectual property rights claimed by third parties. It is the responsibility of users of the service to ensure that their exploitation of the data does not infringe the rights of such third parties. The developers of PSSMSearch can neither comment on the validity of their claims nor grant unrestricted permission regarding the use of the data.
  9. Any feedback on the service is welcome.
  10. The developers of PSSMSearch are not liable to you or third parties claiming through you, for any loss or damage.
  11. The developers of PSSMSearch reserves the right to alter these terms at any time in order to ensure their appropriateness to the PSSMSearch mission.

3rd-party licences

This web service uses the following libraries and resources:

  • Colors from www.ColorBrewer.org by Cynthia A. Brewer, Geography, Pennsylvania State University.
  • pandas 0.15.1 BSD
  • SQLAlchemy 0.9.8 MIT License
  • alembic 0.6.7 MIT
  • futures 2.2.0 BSD
  • pyramid 1.5.2 BSD-derived (http://www.repoze.org/LICENSE.txt)
  • cornice 0.17 MPLv2.0
  • waitress 0.8.9 ZPL 2.1
  • colander 1.0 BSD-derived (http://www.repoze.org/LICENSE.txt)
  • WebTest 2.0.18 MIT
  • requests 2.6.0 Apache 2.0
  • psycopg2 2.5.4 LGPL with exceptions or ZPL
  • numpy 1.9.1 BSD
  • biopython 1.64 Biopython License Agreement or BSD
  • scipy 0.13.0b1 BSD
  • pyramid-exclog 0.8 BSD-derived (http://www.repoze.org/LICENSE.txt)
  • EmberJS MIT
  • Bootstrap MIT
  • Grunt MIT
  • Font Awesome MIT
  • Jquery MIT
  • FileSaver MIT
  • StickyTableHeaders MIT
  • Sentry BSD
  • pq MIT
  • autoprefixer MIT
  • babel-plugin-lodash MIT
  • babel-plugin-react-css-modules BSD-3-Clause
  • babel-plugin-transform-react-remove-prop-types MIT
  • babel-preset-env MIT
  • babel-runtime MIT
  • classnames MIT
  • cookies-eu-banner MIT
  • css-loader MIT
  • d3-scale BSD-3-Clause
  • deep-equal MIT
  • expose-loader MIT
  • fast-memoize MIT
  • flexbox-react MIT
  • history MIT
  • html-webpack-plugin MIT
  • immutability-helper MIT
  • lodash-es MIT
  • lodash MIT
  • node-sass MIT
  • pluralize MIT
  • postcss MIT
  • promise-polyfill MIT
  • prop-types MIT
  • react-copy-to-clipboard MIT
  • react-dom MIT
  • react-helmet MIT
  • react-hot-loader MIT
  • react-redux MIT
  • react MIT
  • redux-act Apache-2.0
  • redux-batched-actions MIT
  • redux-logger MIT
  • redux-thunk MIT
  • redux MIT
  • sass-loader MIT
  • save-svg-as-png MIT
  • semantic-ui-css MIT
  • semantic-ui-react MIT
  • webpack MIT
  • whatwg-fetch MIT

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The role of this cookie is to count the users and to distinguish the new users from the returning users. Expiration: 2 years.
The role of this cookie is to survey the frequency of requests. Expiration: 10 minutes.

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Contact information are available here. You can also report issues on Bitbucket: