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Protein homology detection by profile based fragment matching
Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry. (Sven Hovmöller)
Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry. (Sven Hovmöller)
Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
(English)Manuscript (preprint) (Other academic)
Keyword [en]
fragment matching; remote homology; profile-profile score; shape strings
National Category
Bioinformatics and Systems Biology
Research subject
Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-34097OAI: oai:DiVA.org:su-34097DiVA: diva2:284215
Projects
protein structure prediction
Available from: 2010-01-05 Created: 2010-01-05 Last updated: 2011-01-04Bibliographically approved
In thesis
1. Protein structure prediction: Zinc-binding sites, one-dimensional structure and remote homology
Open this publication in new window or tab >>Protein structure prediction: Zinc-binding sites, one-dimensional structure and remote homology
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Predicting the three-dimensional (3D) structure of proteins is a central problem in biology. These computationally predicted 3D protein structures have been successfully applied in many fields of biomedicine, e.g. family assignments and drug discovery. The accurate detection of remotely homologous templates is critical for the successful prediction of the 3D structure of proteins. Also, the prediction of one-dimensional (1D) protein structures such as secondary structures and shape strings are useful for predicting the 3D structure of proteins and important for understanding the sequence-structure relationship. In addition, the prediction of the functional sites of proteins, such as metal-binding sites, can not only reveal the important function of proteins (even in the absence of the 3D structure) but also facilitate the prediction of the 3D structure.

Here, three novel methods in the field of protein structure prediction are presented: PREDZINC, a method for predicting zinc-binding sites in proteins; Frag1D, a method for predicting the 1D structure of proteins; and FragMatch, a method for detecting remotely homologous proteins. These methods compete satisfactorily with the best methods previously published and contribute to the task of protein structure prediction.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2010. 81 p.
Keyword
protein structure prediction, zinc-binding, profile, homology detection, shape string
National Category
Bioinformatics and Systems Biology Biochemistry and Molecular Biology Biochemistry and Molecular Biology
Research subject
Structural Chemistry
Identifiers
urn:nbn:se:su:diva-34094 (URN)978-91-7155-984-5 (ISBN)
Public defence
2010-02-09, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Magnélisalen, 10:00 (English)
Opponent
Supervisors
Projects
Protein structure prediction
Note
At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.Available from: 2010-01-18 Created: 2010-01-05 Last updated: 2010-12-29Bibliographically approved

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