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Protein Structure Prediction: Model Building and Quality Assessment
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proteins play a crucial roll in all biological processes. The wide range of protein functions is made possible through the many different conformations that the protein chain can adopt. The structure of a protein is extremely important for its function, but to determine the structure of protein experimentally is both difficult and time consuming. In fact with the current methods it is not possible to study all the billions of proteins in the world by experiments. Hence, for the vast majority of proteins the only way to get structural information is through the use of a method that predicts the structure of a protein based on the amino acid sequence.

This thesis focuses on improving the current protein structure prediction methods by combining different prediction approaches together with machine-learning techniques. This work has resulted in some of the best automatic servers in world – Pcons and Pmodeller. As a part of the improvement of our automatic servers, I have also developed one of the best methods for predicting the quality of a protein model – ProQ. In addition, I have also developed methods to predict the local quality of a protein, based on the structure – ProQres and based on evolutionary information – ProQprof. Finally, I have also performed the first large-scale benchmark of publicly available homology modeling programs.

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik , 2005. , 54 p.
Keyword [en]
protein structure prediction
Keyword [sv]
proteinstrukturförutsägelse
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:su:diva-649ISBN: 91-7155-121-2 (print)OAI: oai:DiVA.org:su-649DiVA: diva2:196554
Public defence
2005-09-30, sal FD5, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 10:00
Opponent
Supervisors
Available from: 2005-09-07 Created: 2005-09-07Bibliographically approved
List of papers
1. Can correct protein models be identified?
Open this publication in new window or tab >>Can correct protein models be identified?
2003 In: Protein Science, ISSN 0961-8368, Vol. 12, no 5, 1073-1086 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24035 (URN)
Note
Part of urn:nbn:se:su:diva-649Available from: 2005-09-07 Created: 2005-09-07Bibliographically approved
2. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller
Open this publication in new window or tab >>Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller
2003 In: Proteins: Structure, Function, and Genetics, ISSN 0887-3585, Vol. 53, no S6, 534-541 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24036 (URN)
Note
Part of urn:nbn:se:su:diva-649Available from: 2005-09-07 Created: 2005-09-07Bibliographically approved
3. Identification of correct regions in protein models using structural, evolutionary and consensus information
Open this publication in new window or tab >>Identification of correct regions in protein models using structural, evolutionary and consensus information
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-24037 (URN)
Note
Part of urn:nbn:se:su:diva-649Available from: 2005-09-07 Created: 2005-09-07 Last updated: 2010-01-13Bibliographically approved
4. Pcons5: combining consensus, structural evaluation and fold recognition scores
Open this publication in new window or tab >>Pcons5: combining consensus, structural evaluation and fold recognition scores
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-24038 (URN)
Note
Part of urn:nbn:se:su:diva-649Available from: 2005-09-07 Created: 2005-09-07 Last updated: 2010-01-13Bibliographically approved
5. All are not equal: a benchmark of different homology modeling programs
Open this publication in new window or tab >>All are not equal: a benchmark of different homology modeling programs
2005 In: Protein Science, ISSN 0961-8368, Vol. 14, no 5, 1315-1327 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24039 (URN)
Note
Part of urn:nbn:se:su:diva-649Available from: 2005-09-07 Created: 2005-09-07Bibliographically approved

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