Arne Elofsson, Ph.D. - Publications

Affiliations: 
Biochemistry and Biophysics Stockholm University, Stockholm, Stockholms län, Sweden 
Area:
Membrane proteins, Bioinformatics, Biochemistry, Protein structure prediction, Protein evolution
Website:
http://bioinfo.se

147 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Delucchi M, Schaper E, Sachenkova O, Elofsson A, Anisimova M. A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. Genes. 11. PMID 32283633 DOI: 10.3390/genes11040407  1
2019 Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, et al. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Research. PMID 31713636 DOI: 10.1093/nar/gkz975  0.56
2019 Almagro Armenteros JJ, Salvatore M, Emanuelsson O, Winther O, von Heijne G, Elofsson A, Nielsen H. Detecting sequence signals in targeting peptides using deep learning. Life Science Alliance. 2. PMID 31570514 DOI: 10.26508/lsa.201900429  1
2019 Ndi M, Masuyer G, Dawitz H, Carlström A, Michel M, Elofsson A, Rapp M, Stenmark P, Ott M. Structural basis for the interaction of the chaperone Cbp3 with newly synthesized cytochrome during mitochondrial respiratory chain assembly. The Journal of Biological Chemistry. PMID 31537648 DOI: 10.1074/jbc.RA119.010483  0.6
2019 Basile W, Salvatore M, Bassot C, Elofsson A. Why do eukaryotic proteins contain more intrinsically disordered regions? Plos Computational Biology. 15: e1007186. PMID 31329574 DOI: 10.1371/journal.pcbi.1007186  0.84
2019 Cheng J, Choe MH, Elofsson A, Han KS, Hou J, Maghrabi AHA, McGuffin LJ, Menéndez-Hurtado D, Olechnovič K, Schwede T, Studer G, Uziela K, Venclovas Č, Wallner B. Estimation of model accuracy in CASP13. Proteins. PMID 31265154 DOI: 10.1002/prot.25767  1
2019 Bassot C, Menendez Hurtado D, Elofsson A. Using PconsC4 and PconsFold2 to Predict Protein Structure. Current Protocols in Bioinformatics. e75. PMID 31063641 DOI: 10.1002/cpbi.75  0.32
2019 Lamb J, Jarmolinska AI, Michel M, Menéndez-Hurtado D, Sulkowska JI, Elofsson A. PconsFam: An interactive database of structure predictions of Pfam families. Journal of Molecular Biology. PMID 30796988 DOI: 10.1016/j.jmb.2019.01.047  0.6
2019 Elofsson A, Hess B, Lindahl E, Onufriev A, van der Spoel D, Wallqvist A. Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. Plos Computational Biology. 15: e1006649. PMID 30653494 DOI: 10.1371/journal.pcbi.1006649  0.64
2018 Michel M, Hurtado DM, Elofsson A. PconsC4: fast, accurate, and hassle-free contact predictions. Bioinformatics (Oxford, England). PMID 30590407 DOI: 10.1093/bioinformatics/bty1036  0.6
2018 Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A. Improved protein model quality assessments by changing the target function. Proteins. PMID 29524250 DOI: 10.1002/prot.25492  1
2017 Tsirigos KD, Govindarajan S, Bassot C, Västermark Å, Lamb J, Shu N, Elofsson A. Topology of membrane proteins-predictions, limitations and variations. Current Opinion in Structural Biology. 50: 9-17. PMID 29100082 DOI: 10.1016/j.sbi.2017.10.003  0.8
2017 Elofsson A, Joo K, Keasar C, Lee J, Maghrabi AHA, Manavalan B, McGuffin LJ, Ménendez Hurtado D, Mirabello C, Pilstål R, Sidi T, Uziela K, Wallner B. Methods for estimation of model accuracy in CASP12. Proteins. PMID 28975666 DOI: 10.1002/prot.25395  1
2017 Salvatore M, Shu N, Elofsson A. The SubCons web-server: A user friendly web interface for state-of-the-art subcellular localization prediction. Protein Science : a Publication of the Protein Society. PMID 28901589 DOI: 10.1002/pro.3297  0.8
2017 Michel M, Menéndez Hurtado D, Uziela K, Elofsson A. Large-scale structure prediction by improved contact predictions and model quality assessment. Bioinformatics (Oxford, England). 33: i23-i29. PMID 28881974 DOI: 10.1093/bioinformatics/btx239  0.8
2017 Michel M, Skwark MJ, Menéndez Hurtado D, Ekeberg M, Elofsson A. Predicting accurate contacts in thousands of Pfam domain families using PconsC3. Bioinformatics (Oxford, England). PMID 28535189 DOI: 10.1093/bioinformatics/btx332  1
2017 Salvatore M, Warholm P, Shu N, Basile W, Elofsson A. SubCons: a new ensemble method for improved human subcellular localization predictions. Bioinformatics (Oxford, England). PMID 28407043 DOI: 10.1093/bioinformatics/btx219  0.84
2017 Basile W, Sachenkova O, Light S, Elofsson A. High GC content causes orphan proteins to be intrinsically disordered. Plos Computational Biology. 13: e1005375. PMID 28355220 DOI: 10.1371/journal.pcbi.1005375  1
2017 Dimou NL, Tsirigos KD, Elofsson A, Bagos PG. GWAR: Robust Analysis and Meta-Analysis of Genome-Wide Association Studies. Bioinformatics (Oxford, England). PMID 28108451 DOI: 10.1093/bioinformatics/btx008  0.48
2017 Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A. ProQ3D: Improved model quality assessments using Deep Learning. Bioinformatics (Oxford, England). PMID 28052925 DOI: 10.1093/bioinformatics/btw819  1
2016 Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27965415 DOI: 10.1093/nar/gkw1279  0.48
2016 Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27899601 DOI: 10.1093/nar/gkw1056  0.48
2016 Uziela K, Shu N, Wallner B, Elofsson A. ProQ3: Improved model quality assessments using Rosetta energy terms. Scientific Reports. 6: 33509. PMID 27698390 DOI: 10.1038/srep33509  1
2016 Tsirigos KD, Elofsson A, Bagos PG. PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. Bioinformatics (Oxford, England). 32: i665-i671. PMID 27587687 DOI: 10.1093/bioinformatics/btw444  0.48
2016 Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A. Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins. Bioinformatics (Oxford, England). PMID 26794316 DOI: 10.1093/bioinformatics/btw025  1
2015 Peters C, Tsirigos KD, Shu N, Elofsson A. Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics (Oxford, England). PMID 26644416 DOI: 10.1093/bioinformatics/btv709  1
2015 Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, et al. Molecular architecture of the active mitochondrial protein gate. Science (New York, N.Y.). 349: 1544-8. PMID 26404837 DOI: 10.1126/science.aac6428  1
2015 De Marothy MT, Elofsson A. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding. Protein Science : a Publication of the Protein Society. 24: 1057-74. PMID 25970811 DOI: 10.1002/pro.2698  1
2015 Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Research. 43: W401-7. PMID 25969446 DOI: 10.1093/nar/gkv485  1
2015 Mirzadeh K, Martínez V, Toddo S, Guntur S, Herrgård MJ, Elofsson A, Nørholm MH, Daley DO. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction. Acs Synthetic Biology. PMID 25951437 DOI: 10.1021/acssynbio.5b00033  1
2015 Hayat S, Sander C, Marks DS, Elofsson A. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences. Proceedings of the National Academy of Sciences of the United States of America. 112: 5413-8. PMID 25858953 DOI: 10.1073/pnas.1419956112  1
2014 Skwark MJ, Raimondi D, Michel M, Elofsson A. Improved contact predictions using the recognition of protein like contact patterns. Plos Computational Biology. 10: e1003889. PMID 25375897 DOI: 10.1371/journal.pcbi.1003889  1
2014 Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics (Oxford, England). 30: i482-8. PMID 25161237 DOI: 10.1093/bioinformatics/btu458  1
2014 Light S, Basile W, Elofsson A. Orphans and new gene origination, a structural and evolutionary perspective. Current Opinion in Structural Biology. 26: 73-83. PMID 24934869 DOI: 10.1016/j.sbi.2014.05.006  1
2014 Virkki MT, Peters C, Nilsson D, Sörensen T, Cristobal S, Wallner B, Elofsson A. The positive inside rule is stronger when followed by a transmembrane helix. Journal of Molecular Biology. 426: 2982-91. PMID 24927974 DOI: 10.1016/j.jmb.2014.06.002  1
2014 Virkki M, Boekel C, Illergård K, Peters C, Shu N, Tsirigos KD, Elofsson A, von Heijne G, Nilsson I. Large tilts in transmembrane helices can be induced during tertiary structure formation. Journal of Molecular Biology. 426: 2529-38. PMID 24793448 DOI: 10.1016/j.jmb.2014.04.020  1
2014 Virkki MT, Agrawal N, Edsbäcker E, Cristobal S, Elofsson A, Kauko A. Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Science : a Publication of the Protein Society. 23: 981-92. PMID 24777974 DOI: 10.1002/pro.2483  1
2014 Peters C, Elofsson A. Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins. 82: 2190-8. PMID 24753217 DOI: 10.1002/prot.24582  1
2013 Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A. Protein expansion is primarily due to indels in intrinsically disordered regions. Molecular Biology and Evolution. 30: 2645-53. PMID 24037790 DOI: 10.1093/molbev/mst157  1
2013 Skwark MJ, Elofsson A. PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. Bioinformatics (Oxford, England). 29: 1817-8. PMID 23677942 DOI: 10.1093/bioinformatics/btt272  1
2013 Skwark MJ, Abdel-Rehim A, Elofsson A. PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics (Oxford, England). 29: 1815-6. PMID 23658418 DOI: 10.1093/bioinformatics/btt259  1
2013 Light S, Elofsson A. The impact of splicing on protein domain architecture. Current Opinion in Structural Biology. 23: 451-8. PMID 23562110 DOI: 10.1016/j.sbi.2013.02.013  1
2013 Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A. Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics. 13: 1467-80. PMID 23512833 DOI: 10.1002/pmic.201200517  1
2013 Light S, Sagit R, Ekman D, Elofsson A. Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins. Biochimica Et Biophysica Acta. 1834: 890-7. PMID 23333420 DOI: 10.1016/j.bbapap.2013.01.002  1
2013 Jurkowski W, Yazdi S, Elofsson A. Ligand binding properties of human galanin receptors. Molecular Membrane Biology. 30: 206-16. PMID 23237663 DOI: 10.3109/09687688.2012.750384  1
2013 Bañó-Polo M, Martínez-Gil L, Wallner B, Nieva JL, Elofsson A, Mingarro I. Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. Journal of Molecular Biology. 425: 830-40. PMID 23228331 DOI: 10.1016/j.jmb.2012.12.001  1
2013 Imai K, Hayat S, Sakiyama N, Fujita N, Tomii K, Elofsson A, Horton P. Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods in Molecular Biology (Clifton, N.J.). 939: 115-40. PMID 23192545 DOI: 10.1007/978-1-62703-107-3_10  1
2012 Hayat S, Elofsson A. Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions. Bioinformatics (Oxford, England). 28: i90-6. PMID 22689784 DOI: 10.1093/bioinformatics/bts233  1
2012 Tsirigos KD, Hennerdal A, Käll L, Elofsson A. A guideline to proteome-wide α-helical membrane protein topology predictions. Proteomics. 12: 2282-94. PMID 22685073 DOI: 10.1002/pmic.201100495  1
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/pro.2071  1
2012 Light S, Sagit R, Ithychanda SS, Qin J, Elofsson A. The evolution of filamin-a protein domain repeat perspective. Journal of Structural Biology. 179: 289-98. PMID 22414427 DOI: 10.1016/j.jsb.2012.02.010  1
2012 Hayat S, Elofsson A. BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. Bioinformatics (Oxford, England). 28: 516-22. PMID 22247276 DOI: 10.1093/bioinformatics/btr710  1
2012 Contreras FX, Ernst AM, Haberkant P, Björkholm P, Lindahl E, Gönen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brügger B. Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature. 481: 525-9. PMID 22230960 DOI: 10.1038/nature10742  1
2012 Nørholm MH, Light S, Virkki MT, Elofsson A, von Heijne G, Daley DO. Manipulating the genetic code for membrane protein production: what have we learnt so far? Biochimica Et Biophysica Acta. 1818: 1091-6. PMID 21884679 DOI: 10.1016/j.bbamem.2011.08.018  1
2011 Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (London, England : 1993). 19: 1108-26. PMID 21827947 DOI: 10.1016/j.str.2011.05.012  1
2011 Hedin LE, Illergård K, Elofsson A. An introduction to membrane proteins. Journal of Proteome Research. 10: 3324-31. PMID 21815691 DOI: 10.1021/pr200145a  1
2011 Basmarke-Wehelie R, Sjölinder H, Jurkowski W, Elofsson A, Arnqvist A, Engstrand L, Hagner M, Wallin E, Guan N, Kuranasekera H, Aro H, Jonsson AB. The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity. Gastroenterology. 141: 918-28. PMID 21699774 DOI: 10.1053/j.gastro.2011.05.009  1
2011 Shu N, Elofsson A. KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics (Oxford, England). 27: 1702-3. PMID 21505030 DOI: 10.1093/bioinformatics/btr235  1
2011 Hennerdal A, Elofsson A. Rapid membrane protein topology prediction. Bioinformatics (Oxford, England). 27: 1322-3. PMID 21493661 DOI: 10.1093/bioinformatics/btr119  1
2011 Larsson P, Skwark MJ, Wallner B, Elofsson A. Improved predictions by Pcons.net using multiple templates. Bioinformatics (Oxford, England). 27: 426-7. PMID 21149277 DOI: 10.1093/bioinformatics/btq664  1
2011 Illergård K, Kauko A, Elofsson A. Why are polar residues within the membrane core evolutionary conserved? Proteins. 79: 79-91. PMID 20938980 DOI: 10.1002/prot.22859  1
2010 Lima Mde F, Eloy NB, Pegoraro C, Sagit R, Rojas C, Bretz T, Vargas L, Elofsson A, de Oliveira AC, Hemerly AS, Ferreira PC. Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. Bmc Plant Biology. 10: 254. PMID 21087491 DOI: 10.1186/1471-2229-10-254  1
2010 Hennerdal A, Falk J, Lindahl E, Elofsson A. Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Science : a Publication of the Protein Society. 19: 2305-18. PMID 20882639 DOI: 10.1002/pro.510  1
2010 Runesson J, Sollenberg UE, Jurkowski W, Yazdi S, Eriksson EE, Elofsson A, Langel U. Determining receptor-ligand interaction of human galanin receptor type 3. Neurochemistry International. 57: 804-11. PMID 20817064 DOI: 10.1016/j.neuint.2010.08.018  1
2010 Björklund AK, Light S, Sagit R, Elofsson A. Nebulin: a study of protein repeat evolution. Journal of Molecular Biology. 402: 38-51. PMID 20643138 DOI: 10.1016/j.jmb.2010.07.011  1
2010 Illergård K, Callegari S, Elofsson A. MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane. Bmc Bioinformatics. 11: 333. PMID 20565847 DOI: 10.1186/1471-2105-11-333  1
2010 Kauko A, Hedin LE, Thebaud E, Cristobal S, Elofsson A, von Heijne G. Repositioning of transmembrane alpha-helices during membrane protein folding. Journal of Molecular Biology. 397: 190-201. PMID 20109468 DOI: 10.1016/j.jmb.2010.01.042  1
2010 Ekman D, Elofsson A. Identifying and quantifying orphan protein sequences in fungi. Journal of Molecular Biology. 396: 396-405. PMID 19944701 DOI: 10.1016/j.jmb.2009.11.053  1
2010 Hedin LE, Ojemalm K, Bernsel A, Hennerdal A, Illergård K, Enquist K, Kauko A, Cristobal S, von Heijne G, Lerch-Bader M, Nilsson I, Elofsson A. Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. Journal of Molecular Biology. 396: 221-9. PMID 19931281 DOI: 10.1016/j.jmb.2009.11.036  1
2009 Larsson P, Skwark MJ, Wallner B, Elofsson A. Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins. 77: 167-72. PMID 19544566 DOI: 10.1002/prot.22476  1
2009 Illergård K, Ardell DH, Elofsson A. Structure is three to ten times more conserved than sequence--a study of structural response in protein cores. Proteins. 77: 499-508. PMID 19507241 DOI: 10.1002/prot.22458  1
2009 Michino M, Abola E, Brooks CL, Dixon JS, Moult J, Stevens RC. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews. Drug Discovery. 8: 455-63. PMID 19461661 DOI: 10.1038/nrd2877  1
2009 Bernsel A, Viklund H, Hennerdal A, Elofsson A. TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Research. 37: W465-8. PMID 19429891 DOI: 10.1093/nar/gkp363  1
2008 Viklund H, Bernsel A, Skwark M, Elofsson A. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics (Oxford, England). 24: 2928-9. PMID 18945683 DOI: 10.1093/bioinformatics/btn550  1
2008 Björklund AK, Light S, Hedin L, Elofsson A. Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics. 8: 4657-67. PMID 18924110 DOI: 10.1002/pmic.200800150  1
2008 Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. Arrangements in the modular evolution of proteins. Trends in Biochemical Sciences. 33: 444-51. PMID 18656364 DOI: 10.1016/j.tibs.2008.05.008  1
2008 Kauko A, Illergård K, Elofsson A. Coils in the membrane core are conserved and functionally important. Journal of Molecular Biology. 380: 170-80. PMID 18511074 DOI: 10.1016/j.jmb.2008.04.052  1
2008 Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A. Prediction of membrane-protein topology from first principles. Proceedings of the National Academy of Sciences of the United States of America. 105: 7177-81. PMID 18477697 DOI: 10.1073/pnas.0711151105  1
2008 Viklund H, Elofsson A. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics (Oxford, England). 24: 1662-8. PMID 18474507 DOI: 10.1093/bioinformatics/btn221  1
2008 Larsson P, Wallner B, Lindahl E, Elofsson A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein Science : a Publication of the Protein Society. 17: 990-1002. PMID 18441233 DOI: 10.1110/ps.073344908  1
2008 Papaloukas C, Granseth E, Viklund H, Elofsson A. Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Science : a Publication of the Protein Society. 17: 271-8. PMID 18096645 DOI: 10.1110/ps.073036108  1
2008 Bernsel A, Viklund H, Elofsson A. Remote homology detection of integral membrane proteins using conserved sequence features. Proteins. 71: 1387-99. PMID 18076048 DOI: 10.1002/prot.21825  1
2008 Wallner B, Elofsson A. Quality Assessment of Protein Models Prediction of Protein Structures, Functions, and Interactions. 143-157. DOI: 10.1002/9780470741894.ch6  1
2007 Wallner B, Elofsson A. Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins. 69: 184-93. PMID 17894353 DOI: 10.1002/prot.21774  1
2007 Ekman D, Björklund AK, Elofsson A. Quantification of the elevated rate of domain rearrangements in metazoa. Journal of Molecular Biology. 372: 1337-48. PMID 17689563 DOI: 10.1016/j.jmb.2007.06.022  1
2007 Wallner B, Larsson P, Elofsson A. Pcons.net: protein structure prediction meta server. Nucleic Acids Research. 35: W369-74. PMID 17584798 DOI: 10.1093/nar/gkm319  1
2007 Elofsson A, von Heijne G. Membrane protein structure: prediction versus reality. Annual Review of Biochemistry. 76: 125-40. PMID 17579561 DOI: 10.1146/annurev.biochem.76.052705.163539  1
2007 Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA. Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biology. 8: 213. PMID 17521457 DOI: 10.1186/gb-2007-8-5-213  1
2006 Björklund AK, Ekman D, Elofsson A. Expansion of protein domain repeats. Plos Computational Biology. 2: e114. PMID 16933986 DOI: 10.1371/journal.pcbi.0020114  1
2006 Granseth E, Viklund H, Elofsson A. ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Bioinformatics (Oxford, England). 22: e191-6. PMID 16873471 DOI: 10.1093/bioinformatics/btl206  1
2006 Ohlson T, Aggarwal V, Elofsson A, MacCallum RM. Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. Bmc Bioinformatics. 7: 357. PMID 16869963 DOI: 10.1186/1471-2105-7-357  1
2006 Viklund H, Granseth E, Elofsson A. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. Journal of Molecular Biology. 361: 591-603. PMID 16860824 DOI: 10.1016/j.jmb.2006.06.037  1
2006 Amico M, Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D, Krogh A, Fariselli P, Luigi Martelli P, Casadio R. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Research. 34: W169-72. PMID 16844984 DOI: 10.1093/nar/gkl208  1
2006 Ekman D, Light S, Björklund AK, Elofsson A. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biology. 7: R45. PMID 16780599 DOI: 10.1186/gb-2006-7-6-r45  1
2006 Wallner B, Elofsson A. Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Science : a Publication of the Protein Society. 15: 900-13. PMID 16522791 DOI: 10.1110/ps.051799606  1
2006 Björklund A, Thorén A, von Heijne G, Elofsson A. The use of phylogenetic profiles for gene predictions revisited Current Genomics. 7: 79-86. DOI: 10.2174/138920206777304650  1
2005 Light S, Kraulis P, Elofsson A. Preferential attachment in the evolution of metabolic networks. Bmc Genomics. 6: 159. PMID 16281983 DOI: 10.1186/1471-2164-6-159  1
2005 Ohlson T, Elofsson A. ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. Bmc Bioinformatics. 6: 253. PMID 16225676 DOI: 10.1186/1471-2105-6-253  1
2005 Wallner B, Elofsson A. Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics (Oxford, England). 21: 4248-54. PMID 16204344 DOI: 10.1093/bioinformatics/bti702  1
2005 Björklund AK, Ekman D, Light S, Frey-Skött J, Elofsson A. Domain rearrangements in protein evolution. Journal of Molecular Biology. 353: 911-23. PMID 16198373 DOI: 10.1016/j.jmb.2005.08.067  1
2005 Berglund AC, Wallner B, Elofsson A, Liberles DA. Tertiary windowing to detect positive diversifying selection. Journal of Molecular Evolution. 60: 499-504. PMID 15883884 DOI: 10.1007/s00239-004-0223-4  1
2005 Wallner B, Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Science : a Publication of the Protein Society. 14: 1315-27. PMID 15840834 DOI: 10.1110/ps.041253405  1
2005 Ekman D, Björklund AK, Frey-Skött J, Elofsson A. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. Journal of Molecular Biology. 348: 231-43. PMID 15808866 DOI: 10.1016/j.jmb.2005.02.007  1
2005 Granseth E, von Heijne G, Elofsson A. A study of the membrane-water interface region of membrane proteins. Journal of Molecular Biology. 346: 377-85. PMID 15663952 DOI: 10.1016/j.jmb.2004.11.036  1
2004 Ohlson T, Wallner B, Elofsson A. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins. 57: 188-97. PMID 15326603 DOI: 10.1002/prot.20184  1
2004 Viklund H, Elofsson A. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Science : a Publication of the Protein Society. 13: 1908-17. PMID 15215532 DOI: 10.1110/ps.04625404  1
2004 Wallner B, Fang H, Ohlson T, Frey-Skött J, Elofsson A. Using evolutionary information for the query and target improves fold recognition. Proteins. 54: 342-50. PMID 14696196 DOI: 10.1002/prot.10565  1
2003 Rychlewski L, Fischer D, Elofsson A. LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins. 53: 542-7. PMID 14579344 DOI: 10.1002/prot.10535  1
2003 Wallner B, Fang H, Elofsson A. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins. 53: 534-41. PMID 14579343 DOI: 10.1002/prot.10536  1
2003 Fischer D, Rychlewski L, Dunbrack RL, Ortiz AR, Elofsson A. CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins. 53: 503-16. PMID 14579340 DOI: 10.1002/prot.10538  1
2003 Emanuelsson O, Elofsson A, von Heijne G, Cristóbal S. In silico prediction of the peroxisomal proteome in fungi, plants and animals. Journal of Molecular Biology. 330: 443-56. PMID 12823981 DOI: 10.1016/S0022-2836(03)00553-9  1
2003 Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (Oxford, England). 19: 1015-8. PMID 12761065 DOI: 10.1093/bioinformatics/btg124  1
2003 Wallner B, Elofsson A. Can correct protein models be identified? Protein Science : a Publication of the Protein Society. 12: 1073-86. PMID 12717029 DOI: 10.1110/ps.0236803  1
2002 Dönnes P, Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. Bmc Bioinformatics. 3: 25. PMID 12225620 DOI: 10.1186/1471-2105-3-25  1
2002 Milchert LE, Liberles DA, Elofsson A. The salmon genome (and other issues in bioinformatics). Genome Biology. 3: REPORTS4022. PMID 12184805  1
2002 Hedman M, Deloof H, Von Heijne G, Elofsson A. Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Science : a Publication of the Protein Society. 11: 652-8. PMID 11847287 DOI: 10.1110/ps.39402  1
2002 Elofsson A. A study on protein sequence alignment quality. Proteins. 46: 330-9. PMID 11835508 DOI: 10.1002/prot.10043  1
2002 Liberles DA, Thorén A, von Heijne G, Elofsson A. The use of phylogenetic profiles for gene predictions Current Genomics. 3: 131-137. DOI: 10.2174/1389202023350499  1
2001 Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins. 184-91. PMID 11835496 DOI: 10.1002/prot.10039  1
2001 Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack RL. CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins. 171-83. PMID 11835495 DOI: 10.1002/prot.10036  1
2001 Lundström J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Science : a Publication of the Protein Society. 10: 2354-62. PMID 11604541 DOI: 10.1110/ps.08501  1
2001 Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. A study of quality measures for protein threading models. Bmc Bioinformatics. 2: 5. PMID 11545673 DOI: 10.1186/1471-2105-2-5  1
2001 Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. Structure prediction meta server. Bioinformatics (Oxford, England). 17: 750-1. PMID 11524381  1
2001 Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Science : a Publication of the Protein Society. 10: 352-61. PMID 11266621 DOI: 10.1110/ps.40501  1
2001 Eriksson O, Zhou Y, Elofsson A. Side chain-positioning as an integer programming problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2149: 128-141. DOI: 10.1007/3-540-44696-6_10  1
2000 Fischer D, Elofsson A, Rychlewski L. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2. Protein Engineering. 13: 667-70. PMID 11112504  1
2000 Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics (Oxford, England). 16: 776-85. PMID 11108700  1
2000 Lindahl E, Elofsson A. Identification of related proteins on family, superfamily and fold level. Journal of Molecular Biology. 295: 613-25. PMID 10623551 DOI: 10.1006/jmbi.1999.3377  1
1999 Garemyr R, Elofsson A. Study of the electrostatics treatment in molecular dynamics simulations. Proteins. 37: 417-28. PMID 10591101 DOI: 10.1002/(SICI)1097-0134(19991115)37:3<417::AID-PROT9>3.0.CO;2-U  1
1999 Monné M, Nilsson I, Elofsson A, von Heijne G. Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale. Journal of Molecular Biology. 293: 807-14. PMID 10543969 DOI: 10.1006/jmbi.1999.3183  1
1999 Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins. 209-17. PMID 10526371 DOI: 10.1002/(SICI)1097-0134(1999)37:3+<209::AID-PROT27>3.0.CO;2-Y  1
1999 Elofsson A, Sonnhammer EL. A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics (Oxford, England). 15: 480-500. PMID 10383473 DOI: 10.1093/bioinformatics/15.6.480  1
1999 Hargbo J, Elofsson A. Hidden Markov models that use predicted secondary structures for fold recognition. Proteins. 36: 68-76. PMID 10373007 DOI: 10.1002/(SICI)1097-0134(19990701)36:1<68::AID-PROT6>3.0.CO;2-1  1
1999 Zhang XP, Elofsson A, Andreu D, Glaser E. Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70. Journal of Molecular Biology. 288: 177-90. PMID 10329135 DOI: 10.1006/jmbi.1999.2669  1
1998 Seshadri K, Garemyr R, Wallin E, von Heijne G, Elofsson A. Architecture of beta-barrel membrane proteins: analysis of trimeric porins. Protein Science : a Publication of the Protein Society. 7: 2026-32. PMID 9761484 DOI: 10.1002/pro.5560070919  1
1997 Mingarro I, Elofsson A, von Heijne G. Helix-helix packing in a membrane-like environment. Journal of Molecular Biology. 272: 633-41. PMID 9325117 DOI: 10.1006/jmbi.1997.1276  1
1997 Cserzö M, Wallin E, Simon I, von Heijne G, Elofsson A. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Engineering. 10: 673-6. PMID 9278280  1
1997 Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Science : a Publication of the Protein Society. 6: 808-15. PMID 9098890 DOI: 10.1002/pro.5560060407  1
1996 Fischer D, Elofsson A, Rice D, Eisenberg D. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 300-18. PMID 9390240  1
1996 Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D. A study of combined structure/sequence profiles. Folding & Design. 1: 451-61. PMID 9080191 DOI: 10.1016/S1359-0278(96)00061-2  1
1996 Elofsson A, Nilsson L. A 1.2 ns molecular dynamics simulation of the ribonuclease T1-3′-guanosine monophosphate complex Journal of Physical Chemistry. 100: 2480-2488.  1
1995 Elofsson A, Le Grand SM, Eisenberg D. Local moves: an efficient algorithm for simulation of protein folding. Proteins. 23: 73-82. PMID 8539252 DOI: 10.1002/prot.340230109  1
1993 Elofsson A, Nilsson L. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. Journal of Molecular Biology. 233: 766-80. PMID 8411178 DOI: 10.1006/jmbi.1993.1551  1
1993 Elofsson A, Kulinski T, Rigler R, Nilsson L. Site specific point mutation changes specificity: a molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions. Proteins. 17: 161-75. PMID 8265564 DOI: 10.1002/prot.340170206  1
1992 Sander C, Vriend G, Bazan F, Horovitz A, Nakamura H, Ribas L, Finkelstein AV, Lockhart A, Merkl R, Perry LJ. Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida. Proteins. 12: 105-10. PMID 1603799 DOI: 10.1002/prot.340120203  1
1991 Elofsson A, Rigler R, Nilsson L, Roslund J, Krause G, Holmgren A. Motion of aromatic side chains, picosecond fluorescence, and internal energy transfer in Escherichia coli thioredoxin studied by site-directed mutagenesis, time-resolved fluorescence spectroscopy, and molecular dynamics simulations. Biochemistry. 30: 9648-56. PMID 1911751  1
1990 Elofsson A, Nilsson L, Rigler R. Studies on somatostatin with time-resolved spectroscopy and molecular dynamics simulations. International Journal of Peptide and Protein Research. 36: 297-301. PMID 1980672  1
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