Arne Elofsson

Arne Elofsson

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Arne Elofsson

Publications by authors named "Arne Elofsson"

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Estimation of model accuracy in CASP13.

Proteins 2019 Dec 16;87(12):1361-1377. Epub 2019 Jul 16.

Department of Physics, Chemistry, and Biology, Bioinformatics Division, Linköping University, Linköping, Sweden.

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http://dx.doi.org/10.1002/prot.25767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851425PMC
December 2019

Detecting sequence signals in targeting peptides using deep learning.

Life Sci Alliance 2019 Oct 30;2(5). Epub 2019 Sep 30.

Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongen Lyngby, Denmark

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http://dx.doi.org/10.26508/lsa.201900429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769257PMC
October 2019

PconsC4: fast, accurate and hassle-free contact predictions.

Bioinformatics 2019 Aug;35(15):2677-2679

Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty1036DOI Listing
August 2019

Why do eukaryotic proteins contain more intrinsically disordered regions?

PLoS Comput Biol 2019 07 22;15(7):e1007186. Epub 2019 Jul 22.

Science for Life Laboratory, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1007186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6675126PMC
July 2019

PconsFam: An Interactive Database of Structure Predictions of Pfam Families.

J Mol Biol 2019 Jun 21;431(13):2442-2448. Epub 2019 Feb 21.

Science for Life Laboratory and Department of Biochemistry and biophysics, Stockholm University, Tomtebodav 23, 171 21 Solna, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.01.047DOI Listing
June 2019

Using PconsC4 and PconsFold2 to Predict Protein Structure.

Curr Protoc Bioinformatics 2019 06 7;66(1):e75. Epub 2019 May 7.

Department of Biochemistry and Biophysics, Stockholm University and Science for Life Laboratory, Solna, Sweden.

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http://dx.doi.org/10.1002/cpbi.75DOI Listing
June 2019

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.

PLoS Comput Biol 2019 01 17;15(1):e1006649. Epub 2019 Jan 17.

Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006649DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336246PMC
January 2019

Topology of membrane proteins-predictions, limitations and variations.

Curr Opin Struct Biol 2018 06 5;50:9-17. Epub 2017 Nov 5.

Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Swedish e-Science Research Center (SeRC), Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2017.10.003DOI Listing
June 2018

Improved protein model quality assessments by changing the target function.

Proteins 2018 06 15;86(6):654-663. Epub 2018 Apr 15.

Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1002/prot.25492DOI Listing
June 2018

Methods for estimation of model accuracy in CASP12.

Proteins 2018 03 17;86 Suppl 1:361-373. Epub 2017 Oct 17.

Department of Physics, Chemistry, and Biology, Bioinformatics Division, Linköping University, Linköping, 581 83, Sweden.

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http://dx.doi.org/10.1002/prot.25395DOI Listing
March 2018

Predicting accurate contacts in thousands of Pfam domain families using PconsC3.

Bioinformatics 2017 Sep;33(18):2859-2866

Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden.

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https://academic.oup.com/bioinformatics/article/33/18/2859/3
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http://dx.doi.org/10.1093/bioinformatics/btx332DOI Listing
September 2017

Large-scale structure prediction by improved contact predictions and model quality assessment.

Bioinformatics 2017 Jul;33(14):i23-i29

Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btx239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870574PMC
July 2017

ProQ3D: improved model quality assessments using deep learning.

Bioinformatics 2017 May;33(10):1578-1580

Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw819DOI Listing
May 2017

GWAR: robust analysis and meta-analysis of genome-wide association studies.

Bioinformatics 2017 May;33(10):1521-1527

Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.

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http://dx.doi.org/10.1093/bioinformatics/btx008DOI Listing
May 2017

High GC content causes orphan proteins to be intrinsically disordered.

PLoS Comput Biol 2017 03 29;13(3):e1005375. Epub 2017 Mar 29.

Science for Life Laboratory, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1005375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389847PMC
March 2017

ProQ3: Improved model quality assessments using Rosetta energy terms.

Sci Rep 2016 10 4;6:33509. Epub 2016 Oct 4.

Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 171 21 Solna, Sweden.

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https://www.nature.com/articles/srep33509.pdf
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http://arxiv.org/pdf/1602.05832
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http://www.diva-portal.org/smash/record.jsf?pid=diva2:106349
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http://www.nature.com/articles/srep33509
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http://dx.doi.org/10.1038/srep33509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048106PMC
October 2016

PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins.

Bioinformatics 2016 09;32(17):i665-i671

Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece.

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http://dx.doi.org/10.1093/bioinformatics/btw444DOI Listing
September 2016

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.

Bioinformatics 2016 05 21;32(10):1571-3. Epub 2016 Jan 21.

Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and.

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http://dx.doi.org/10.1093/bioinformatics/btw025DOI Listing
May 2016

Improved topology prediction using the terminal hydrophobic helices rule.

Bioinformatics 2016 04 7;32(8):1158-62. Epub 2015 Dec 7.

Department of Biochemistry and Biophysics, Science for Life Laboratory and.

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http://dx.doi.org/10.1093/bioinformatics/btv709DOI Listing
April 2016

Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction.

ACS Synth Biol 2015 Sep 15;4(9):959-65. Epub 2015 May 15.

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2970 Hørsholm, Denmark.

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http://pubs.acs.org/doi/10.1021/acssynbio.5b00033
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http://dx.doi.org/10.1021/acssynbio.5b00033DOI Listing
September 2015

Molecular architecture of the active mitochondrial protein gate.

Science 2015 Sep;349(6255):1544-8

Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan. Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan.

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http://dx.doi.org/10.1126/science.aac6428DOI Listing
September 2015

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

Nucleic Acids Res 2015 Jul 12;43(W1):W401-7. Epub 2015 May 12.

Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden

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http://dx.doi.org/10.1093/nar/gkv485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489233PMC
July 2015

Marginally hydrophobic transmembrane α-helices shaping membrane protein folding.

Protein Sci 2015 Jul 30;24(7):1057-74. Epub 2015 May 30.

Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden.

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http://dx.doi.org/10.1002/pro.2698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500307PMC
July 2015

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Proc Natl Acad Sci U S A 2015 Apr 9;112(17):5413-8. Epub 2015 Apr 9.

Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden

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http://dx.doi.org/10.1073/pnas.1419956112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418893PMC
April 2015

Improved contact predictions using the recognition of protein like contact patterns.

PLoS Comput Biol 2014 Nov 6;10(11):e1003889. Epub 2014 Nov 6.

Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1003889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222596PMC
November 2014

Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?

Proteins 2014 Sep 29;82(9):2190-8. Epub 2014 Apr 29.

Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21, Solna, Sweden.

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http://dx.doi.org/10.1002/prot.24582DOI Listing
September 2014

PconsFold: improved contact predictions improve protein models.

Bioinformatics 2014 Sep;30(17):i482-8

Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden, Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland and Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden, Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland and Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147911PMC
September 2014

The positive inside rule is stronger when followed by a transmembrane helix.

J Mol Biol 2014 Aug 10;426(16):2982-91. Epub 2014 Jun 10.

Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.06.002DOI Listing
August 2014

Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core.

Protein Sci 2014 Jul 14;23(7):981-92. Epub 2014 May 14.

Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden.

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http://doi.wiley.com/10.1002/pro.2483
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http://dx.doi.org/10.1002/pro.2483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4088982PMC
July 2014

Large tilts in transmembrane helices can be induced during tertiary structure formation.

J Mol Biol 2014 Jun 30;426(13):2529-38. Epub 2014 Apr 30.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.04.020DOI Listing
June 2014

Orphans and new gene origination, a structural and evolutionary perspective.

Curr Opin Struct Biol 2014 Jun 13;26:73-83. Epub 2014 Jun 13.

Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Swedish e-Science Research Center (SeRC), Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2014.05.006DOI Listing
June 2014

Protein expansion is primarily due to indels in intrinsically disordered regions.

Mol Biol Evol 2013 Dec 12;30(12):2645-53. Epub 2013 Sep 12.

Science for Life Laboratory, Bioinformatics Infrastructure for Life Sciences, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1093/molbev/mst157DOI Listing
December 2013

PconsC: combination of direct information methods and alignments improves contact prediction.

Bioinformatics 2013 Jul 8;29(14):1815-6. Epub 2013 May 8.

Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btt259DOI Listing
July 2013

PconsD: ultra rapid, accurate model quality assessment for protein structure prediction.

Bioinformatics 2013 Jul 14;29(14):1817-8. Epub 2013 May 14.

Department of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-Science Research Center, Stockholm University, Box 1031, 17121 Solna, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btt272DOI Listing
July 2013

The impact of splicing on protein domain architecture.

Curr Opin Struct Biol 2013 Jun 4;23(3):451-8. Epub 2013 Apr 4.

Science for Life Laboratory, Stockholm University, Box 1031 SE-171 21 Solna, Sweden.

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http://dx.doi.org/10.1016/j.sbi.2013.02.013DOI Listing
June 2013

Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.

Biochim Biophys Acta 2013 May 17;1834(5):890-7. Epub 2013 Jan 17.

Science for Life Laboratory, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1016/j.bbapap.2013.01.002DOI Listing
May 2013

Membrane protein shaving with thermolysin can be used to evaluate topology predictors.

Proteomics 2013 May;13(9):1467-80

Department of Biochemistry and Biophysics, Science for Life Laboratory, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1002/pmic.201200517DOI Listing
May 2013

Ligand binding properties of human galanin receptors.

Mol Membr Biol 2013 Mar 13;30(2):206-16. Epub 2012 Dec 13.

Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.3109/09687688.2012.750384DOI Listing
March 2013

Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion.

J Mol Biol 2013 Feb 7;425(4):830-40. Epub 2012 Dec 7.

Departament de Bioquímica i Biologia Molecular, Universitat de València, E-46100 Burjassot, Spain.

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http://dx.doi.org/10.1016/j.jmb.2012.12.001DOI Listing
February 2013

The evolution of filamin-a protein domain repeat perspective.

J Struct Biol 2012 Sep 10;179(3):289-98. Epub 2012 Mar 10.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Science for Life Laboratory, Bioinformatics Infrastructure for Life Sciences, Stockholm University, SE-17121 Solna, Sweden.

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http://dx.doi.org/10.1016/j.jsb.2012.02.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728663PMC
September 2012

A guideline to proteome-wide α-helical membrane protein topology predictions.

Proteomics 2012 Aug;12(14):2282-94

Stockholm Bioinformatics Center, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1002/pmic.201100495DOI Listing
August 2012

Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions.

Bioinformatics 2012 Jun;28(12):i90-6

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/bts233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371865PMC
June 2012

Manipulating the genetic code for membrane protein production: what have we learnt so far?

Biochim Biophys Acta 2012 Apr 22;1818(4):1091-6. Epub 2011 Aug 22.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Sweden.

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http://dx.doi.org/10.1016/j.bbamem.2011.08.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288168PMC
April 2012

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins.

Bioinformatics 2012 Feb 13;28(4):516-22. Epub 2012 Jan 13.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, SciLifeLab, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btr710DOI Listing
February 2012

Molecular recognition of a single sphingolipid species by a protein's transmembrane domain.

Nature 2012 Jan 9;481(7382):525-9. Epub 2012 Jan 9.

Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature10742DOI Listing
January 2012

The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity.

Gastroenterology 2011 Sep 18;141(3):918-28. Epub 2011 May 18.

Department of Genetics, Microbiology and Toxicology, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1053/j.gastro.2011.05.009DOI Listing
September 2011

An introduction to membrane proteins.

J Proteome Res 2011 Aug;10(8):3324-31

Department of Biochemitry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Science for life laboratory, Swedish E-science Research Center, Stockholm University, 106 91 Stockholm, Sweden.

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http://archive.bioinfo.se/papers/21815691.pdf
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http://dx.doi.org/10.1021/pr200145aDOI Listing
August 2011

KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.

Bioinformatics 2011 Jun 19;27(12):1702-3. Epub 2011 Apr 19.

Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, 106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btr235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106193PMC
June 2011

Rapid membrane protein topology prediction.

Bioinformatics 2011 May;27(9):1322-3

Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btr119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077071PMC
May 2011

Improved predictions by Pcons.net using multiple templates.

Bioinformatics 2011 Feb 11;27(3):426-7. Epub 2010 Dec 11.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Swedish e-Science Research Centre, Stockholm Bioinformatics Centre, SciLifeLab, Stockholm University SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btq664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031036PMC
February 2011

Why are polar residues within the membrane core evolutionary conserved?

Proteins 2011 Jan 11;79(1):79-91. Epub 2010 Oct 11.

Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://doi.wiley.com/10.1002/prot.22859
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http://dx.doi.org/10.1002/prot.22859DOI Listing
January 2011

Determining receptor-ligand interaction of human galanin receptor type 3.

Neurochem Int 2010 Dec 9;57(7):804-11. Epub 2010 Sep 9.

Department of Neurochemistry, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.neuint.2010.08.018DOI Listing
December 2010

Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare.

Protein Sci 2010 Dec;19(12):2305-18

CBR,DBB,SBC, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1002/pro.510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009398PMC
December 2010

Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants.

BMC Plant Biol 2010 Nov 18;10:254. Epub 2010 Nov 18.

Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590 Rio de Janeiro, Brasil.

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http://dx.doi.org/10.1186/1471-2229-10-254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095333PMC
November 2010

Nebulin: a study of protein repeat evolution.

J Mol Biol 2010 Sep 17;402(1):38-51. Epub 2010 Jul 17.

Center for Biological Membrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2010.07.011DOI Listing
September 2010

MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane.

BMC Bioinformatics 2010 Jun 18;11:333. Epub 2010 Jun 18.

Center for Biomembrane Research, Stockholm Bioinformatics Center, Dept of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2105-11-333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904353PMC
June 2010

Repositioning of transmembrane alpha-helices during membrane protein folding.

J Mol Biol 2010 Mar 25;397(1):190-201. Epub 2010 Jan 25.

Center for Biomembrane Research and Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2010.01.042DOI Listing
March 2010

Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context.

J Mol Biol 2010 Feb 18;396(1):221-9. Epub 2009 Nov 18.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2009.11.036DOI Listing
February 2010

Identifying and quantifying orphan protein sequences in fungi.

J Mol Biol 2010 Feb 26;396(2):396-405. Epub 2009 Nov 26.

Stockholm Bioinformatics Center/Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2009.11.053DOI Listing
February 2010

Assessment of global and local model quality in CASP8 using Pcons and ProQ.

Proteins 2009 ;77 Suppl 9:167-72

Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm Bioinformatics Center, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1002/prot.22476DOI Listing
January 2010

Structure is three to ten times more conserved than sequence--a study of structural response in protein cores.

Proteins 2009 Nov;77(3):499-508

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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https://www.researchgate.net/profile/David_Ardell/publicatio
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http://dx.doi.org/10.1002/prot.22458DOI Listing
November 2009

TOPCONS: consensus prediction of membrane protein topology.

Nucleic Acids Res 2009 Jul 8;37(Web Server issue):W465-8. Epub 2009 May 8.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Sweden.

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http://dx.doi.org/10.1093/nar/gkp363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703981PMC
July 2009

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.

Bioinformatics 2008 Dec 22;24(24):2928-9. Epub 2008 Oct 22.

Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btn550DOI Listing
December 2008

Quantitative assessment of the structural bias in protein-protein interaction assays.

Proteomics 2008 Nov;8(22):4657-67

Department of Biochemistry and Biophysics, Center for Biological Membrane Research/Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1002/pmic.200800150DOI Listing
November 2008

Arrangements in the modular evolution of proteins.

Trends Biochem Sci 2008 Sep 24;33(9):444-51. Epub 2008 Jul 24.

Evolutionary Bioinformatics, IEB, University of Münster, Hüfferstrasse 1, Münster, Germany.

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http://dx.doi.org/10.1016/j.tibs.2008.05.008DOI Listing
September 2008

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar.

Bioinformatics 2008 Aug 12;24(15):1662-8. Epub 2008 May 12.

Department of Biochemistry and Biophysics/Center for Biomembrane Research/Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btn221DOI Listing
August 2008

Using multiple templates to improve quality of homology models in automated homology modeling.

Protein Sci 2008 Jun 25;17(6):990-1002. Epub 2008 Apr 25.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1110/ps.073344908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386743PMC
June 2008

Coils in the membrane core are conserved and functionally important.

J Mol Biol 2008 Jun 1;380(1):170-80. Epub 2008 May 1.

Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2008.04.052DOI Listing
June 2008

Remote homology detection of integral membrane proteins using conserved sequence features.

Proteins 2008 May;71(3):1387-99

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1002/prot.21825DOI Listing
May 2008

Prediction of membrane-protein topology from first principles.

Proc Natl Acad Sci U S A 2008 May 13;105(20):7177-81. Epub 2008 May 13.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0711151105
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438223PMC
May 2008

Estimating the length of transmembrane helices using Z-coordinate predictions.

Protein Sci 2008 Feb 20;17(2):271-8. Epub 2007 Dec 20.

Stockholm Bioinformatics Center, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1110/ps.073036108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2222713PMC
February 2008

Prediction of global and local model quality in CASP7 using Pcons and ProQ.

Proteins 2007 ;69 Suppl 8:184-93

Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://doi.wiley.com/10.1002/prot.21774
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January 2008

Quantification of the elevated rate of domain rearrangements in metazoa.

J Mol Biol 2007 Oct 15;372(5):1337-48. Epub 2007 Jun 15.

Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2007.06.022DOI Listing
October 2007

Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia.

Genome Biol 2007 ;8(5):213

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, 5020 Bergen, Norway.

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http://dx.doi.org/10.1186/gb-2007-8-5-213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929130PMC
September 2007

Membrane protein structure: prediction versus reality.

Annu Rev Biochem 2007 ;76:125-40

Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1146/annurev.biochem.76.052705.163539DOI Listing
September 2007

Pcons.net: protein structure prediction meta server.

Nucleic Acids Res 2007 Jul 21;35(Web Server issue):W369-74. Epub 2007 Jun 21.

Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933226PMC
July 2007

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes.

J Mol Biol 2006 Aug 5;361(3):591-603. Epub 2006 Jul 5.

Stockholm Bioinformatics Center/Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360600758
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http://dx.doi.org/10.1016/j.jmb.2006.06.037DOI Listing
August 2006

Expansion of protein domain repeats.

PLoS Comput Biol 2006 Aug 14;2(8):e114. Epub 2006 Jul 14.

Stockholm Bioinformatics Center, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.0020114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1553488PMC
August 2006

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps.

BMC Bioinformatics 2006 Jul 25;7:357. Epub 2006 Jul 25.

Stockholm Bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2105-7-357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1562450PMC
July 2006

ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins.

Bioinformatics 2006 Jul;22(14):e191-6

Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btl206DOI Listing
July 2006

Identification of correct regions in protein models using structural, alignment, and consensus information.

Protein Sci 2006 Apr 7;15(4):900-13. Epub 2006 Mar 7.

Stockholm Bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1110/ps.051799606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242478PMC
April 2006

Pcons5: combining consensus, structural evaluation and fold recognition scores.

Bioinformatics 2005 Dec 4;21(23):4248-54. Epub 2005 Oct 4.

Stockholm Bioinformatics Center, Stockholm University SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/bti702DOI Listing
December 2005

Domain rearrangements in protein evolution.

J Mol Biol 2005 Nov 21;353(4):911-23. Epub 2005 Sep 21.

Stockholm Bioinformatics Center, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2005.08.067DOI Listing
November 2005

Preferential attachment in the evolution of metabolic networks.

BMC Genomics 2005 Nov 10;6:159. Epub 2005 Nov 10.

Stockholm Bioinformatics Center, Department of Biochemistry and Biophyhsics, Albanova University Center, Stockholm University, Stockholm SE-10691, Sweden.

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http://dx.doi.org/10.1186/1471-2164-6-159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1316878PMC
November 2005

ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.

BMC Bioinformatics 2005 Oct 14;6:253. Epub 2005 Oct 14.

Stockholm Blolnformatlcs Center, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2105-6-253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274300PMC
October 2005

All are not equal: a benchmark of different homology modeling programs.

Protein Sci 2005 May;14(5):1315-27

Stockholm Bioinformatics Center, Albanova University Center, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1110/ps.041253405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253266PMC
May 2005

Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions.

J Mol Biol 2005 Apr;348(1):231-43

Stockholm Bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2005.02.007DOI Listing
April 2005

A study of the membrane-water interface region of membrane proteins.

J Mol Biol 2005 Feb 13;346(1):377-85. Epub 2004 Dec 13.

Stockholm Bioinformatics Center, AlbaNova, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jmb.2004.11.036DOI Listing
February 2005

Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods.

Proteins 2004 Oct;57(1):188-97

Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1002/prot.20184DOI Listing
October 2004

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information.

Protein Sci 2004 Jul;13(7):1908-17

Stockholm Bioinformatics Center, Stockholm University, SE-10691 Stockholm, Sweden.

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http://doi.wiley.com/10.1110/ps.04625404
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279939PMC
July 2004