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Comparison of the efficiency of different protein structure refinement techniques
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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2010 (English)Manuscript (preprint) (Other academic)
Place, publisher, year, edition, pages
2010.
Identifiers
URN: urn:nbn:se:su:diva-38247OAI: oai:DiVA.org:su-38247DiVA: diva2:308387
Available from: 2010-04-06 Created: 2010-04-06 Last updated: 2014-11-10Bibliographically approved
In thesis
1. Prediction, modeling, and refinement of protein structure
Open this publication in new window or tab >>Prediction, modeling, and refinement of protein structure
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Accurate predictions of protein structure are important for understanding many processes in cells. The interactions that govern protein folding and structure are complex, and still far from completely understood. However, progress is being made in many areas. Here, efforts to improve the overall quality of protein structure models are described. From a pure evolutionary perspective, in which proteins are viewed in the light of gradually accumulated mutations on the sequence level, it is shown how information from multiple sources helps to create more accurate models. A very simple but surprisingly accurate method for assigning confidence measures for protein structures is also tested. In contrast to models based on evolution, physics based methods view protein structures as the result of physical interactions between atoms. Newly implemented methods are described that both increase the time-scales accessible for molecular dynamics simulations almost 10-fold, and that to some extent might be able to refine protein structures. Finally, I compare the efficiency and properties of different techniques for protein structure refinement.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2010. 64 p.
Keyword
Protein structure prediction, Multiple alignments, Quality assessment, Molecular dynamics, Implicit solvent, Refinement
National Category
Bioinformatics and Systems Biology Bioinformatics (Computational Biology) Theoretical Chemistry
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-38253 (URN)978-91-7447-036-9 (ISBN)
Public defence
2010-05-12, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In press. Paper 5: Manuscript. Available from: 2010-04-20 Created: 2010-04-06 Last updated: 2010-04-09Bibliographically approved

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Larsson, PerBjörkholm, PatrikWallner, BjörnLindahl, ErikElofsson, Arne
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