Publications from the Elofsson lab
Number of publications: 165
Number of citations: 146
H-factor: 8
i10-index: 7
Average Impact Factor: 5.24

Articles ordered by citations
1Baldassarre, F., Menendez Hurtado, D., Elofsson, A. and Azizpour, H. (2021) GraphQA: protein model quality assessment using graph convolutional networks. Bioinformatics 37 (3) : 360-366.
Cited times , Impact Factor: 5.039
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2Elofsson, A. (2021) Toward Characterising the Cellular 3D-Proteome. Front Bioinform 1: 598878.
Cited times , Impact Factor: 0
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3Bryant, P., Pozzati, G., Zhu, W., Shenoy, A., Kundrotas, P. and Elofsson, A. (2022) Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search. Nat Commun 13 (1) : 6028.
Cited times , Impact Factor: 14.92
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4Bryant, P. and Elofsson, A. (2020) Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries. PeerJ 8: e9879.
Cited times , Impact Factor: 2.984
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5Osterlund, N., Vosselman, T., Leppert, A., Graslund, A., Jornvall, H., Ilag, L.L., Marklund, E.G., Elofsson, A., Johansson, J., Sahin, C. and Landreh, M. (2022) Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones. Mol Cell Proteomics 21 (10) : 100413.
Cited times , Impact Factor: 13.156
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6Fischer, D., Elofsson, A., Rychlewski, L., Pazos, F., Valencia, A., Rost, B., Ortiz, A.R. and Dunbrack, Jr., R.L. (2001) CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins Suppl 5: 171-183.
Cited 113 times , Impact Factor: 3.354
 
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7Hedin, L.E., Illergard, K. and Elofsson, A. (2011) An introduction to membrane proteins. J Proteome Res 10 (8) : 3324-3331.
Cited 19 times , Impact Factor: 5.675
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8Elofsson, A and Nilsson, L (1993) Free Energy Perturbations in Ribonuclease T1 Substrate Binding. Study of the Influence of Simulation Length, Internal Freedom and structure in Free Energy Perturbations Molecular Simulations 10 (2-6) : 255-276.
Cited 8 times , Impact Factor: -1
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9Elofsson, A and Nilsson, L (1996) A 1.2 ns Molecular Dynamic Simulation of Ribonuclease T1-3-Guanosine monophosphate complex J Phys Chem 100: 2480-2488.
Cited 4 times , Impact Factor: 3.265
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10David A. Liberles, Anna Thoren, Gunnar von Heijne and Arne Elofsson (2002) The use of Phylogenetic profils for Gene Predictions Current Genomics 3: 131-138.
Cited 2 times , Impact Factor: 0.573
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11Cristobal, S., Zemla, A., Fischer, D., Rychlewski, L. and Elofsson, A. (2001) A study of quality measures for protein threading models. BMC Bioinformatics 2: 5.
Cited 0 times , Impact Factor: 3.493
 
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12Elofsson, A., Kulinski, T., Rigler, R. and Nilsson, L. (1993) 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 (2) : 161-175.
Cited 0 times , Impact Factor: 3.354
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13Milchert, L.E., Liberles, D.A. and Elofsson, A. (2002) The salmon genome (and other issues in bioinformatics). Genome Biol 3 (7) : REPORTS4022.
Cited 0 times , Impact Factor: 10.3
 
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14Hedman, M., Deloof, H., Von Heijne, G. and Elofsson, A. (2002) Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Sci 11 (3) : 652-658.
Cited 0 times , Impact Factor: 3.135
 
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15Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins Suppl 5: 184-191.
Cited 0 times , Impact Factor: 3.354
 
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16Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) Structure prediction meta server. Bioinformatics 17 (8) : 750-751.
Cited 0 times , Impact Factor: 5.039
 
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17Berglund, A.C., Wallner, B., Elofsson, A. and Liberles, D.A. (2005) Tertiary windowing to detect positive diversifying selection. J Mol Evol 60 (4) : 499-504.
Cited 0 times , Impact Factor: 3.234
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18Ginalski, K., Elofsson, A., Fischer, D. and Rychlewski, L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19 (8) : 1015-1018.
Cited 0 times , Impact Factor: 5.039
 
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19Donnes, P. and Elofsson, A. (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3: 25.
Cited 0 times , Impact Factor: 3.493
 
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20Ohlson, T. and Elofsson, A. (2005) ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinformatics 6: 253.
Cited 0 times , Impact Factor: 3.493
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21Elofsson, A. (2002) A study on protein sequence alignment quality. Proteins 46 (3) : 330-339.
Cited 0 times , Impact Factor: 3.354
 
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22Bjorklund, A.K., Ekman, D., Light, S., Frey-Skott, J. and Elofsson, A. (2005) Domain rearrangements in protein evolution. J Mol Biol 353 (4) : 911-923.
Cited 0 times , Impact Factor: 5.501
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23Lundstrom, J., Rychlewski, L., Bujnicki, J. and Elofsson, A. (2001) Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 10 (11) : 2354-2362.
Cited 0 times , Impact Factor: 3.135
 
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24Wallner, B. and Elofsson, A. (2005) All are not equal: a benchmark of different homology modeling programs. Protein Sci 14 (5) : 1315-1327.
Cited 0 times , Impact Factor: 3.135
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25Light, S., Kraulis, P. and Elofsson, A. (2005) Preferential attachment in the evolution of metabolic networks. BMC Genomics 6: 159.
Cited 0 times , Impact Factor: 4.18
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26Wallner, B., Fang, H. and Elofsson, A. (2003) Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins 53 Suppl 6: 534-541.
Cited 0 times , Impact Factor: 3.354
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27Fischer, D, Elofsson, A and Rice, DW, LeGrand, S, Eisenberg, D (1996) Assessing the Performance of Fold Recognition Methods By Means of a Comprehensive Benchmark Proc. Pacific Symposium on Biocomputing, Hawaii, 100: 300-318.
Cited 0 times , Impact Factor: 0
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28Viklund, H. and Elofsson, A. (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci 13 (7) : 1908-1917.
Cited 0 times , Impact Factor: 3.135
 
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29Rychlewski, L., Fischer, D. and Elofsson, A. (2003) LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins 53 Suppl 6: 542-547.
Cited 0 times , Impact Factor: 3.354
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30Wallner, B., Fang, H., Ohlson, T., Frey-Skott, J. and Elofsson, A. (2004) Using evolutionary information for the query and target improves fold recognition. Proteins 54 (2) : 342-350.
Cited 0 times , Impact Factor: 3.354
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31Wallner, B. and Elofsson, A. (2003) Can correct protein models be identified? Protein Sci 12 (5) : 1073-1086.
Cited 0 times , Impact Factor: 3.135
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32Ekman, D., Bjorklund, A.K., Frey-Skott, J. and Elofsson, A. (2005) Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol 348 (1) : 231-243.
Cited 0 times , Impact Factor: 5.501
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33Ekman, D., Light, S., Bjorklund, A.K. and Elofsson, A. (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol 7 (6) : R45.
Cited 0 times , Impact Factor: 10.3
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34Bjorklund, A.K., Ekman, D. and Elofsson, A. (2006) Expansion of Protein Domain Repeats. PLoS Comput Biol 2 (8) : e114.
Cited 0 times , Impact Factor: 6.236
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35Granseth, E., Viklund, H. and Elofsson, A. (2006) ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Bioinformatics 22 (14) : e191-6.
Cited 0 times , Impact Factor: 5.039
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36Viklund, H., Granseth, E. and Elofsson, A. (2006) Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol 361 (3) : 591-603.
Cited 0 times , Impact Factor: 5.501
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37Wallner, B. and Elofsson, A. (2006) Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 15 (4) : 900-913.
Cited 0 times , Impact Factor: 3.135
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38Amico, M., Finelli, M., Rossi, I., Zauli, A., Elofsson, A., Viklund, H., von Heijne, G., Jones, D., Krogh, A., Fariselli, P., Luigi Martelli, P. and Casadio, R. (2006) PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res 34 (Web Server issue) : W169-72.
Cited 0 times , Impact Factor: 6.954
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39Papaloukas, C., Granseth, E., Viklund, H. and Elofsson, A. (2008) Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci 17 (2) : 271-278.
Cited 0 times , Impact Factor: 3.135
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40Fischer, D., Rychlewski, L., Dunbrack, Jr., R.L., Ortiz, A.R. and Elofsson, A. (2003) CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins 53 Suppl 6: 503-516.
Cited 0 times , Impact Factor: 3.354
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41Seshadri, K., Garemyr, R., Wallin, E., von Heijne, G. and Elofsson, A. (1998) Architecture of beta-barrel membrane proteins: analysis of trimeric porins. Protein Sci 7 (9) : 2026-2032.
Cited 0 times , Impact Factor: 3.135
 
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42Wallin, E., Tsukihara, T., Yoshikawa, S., von Heijne, G. and Elofsson, A. (1997) Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci 6 (4) : 808-815.
Cited 0 times , Impact Factor: 3.135
 
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43Mingarro, I., Elofsson, A. and von Heijne, G. (1997) Helix-helix packing in a membrane-like environment. J Mol Biol 272 (4) : 633-641.
Cited 0 times , Impact Factor: 5.501
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44Cserzo, M., Wallin, E., Simon, I., von Heijne, G. and Elofsson, A. (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng 10 (6) : 673-676.
Cited 0 times , Impact Factor: 2.662
 
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45Monne, M., Nilsson, I., Elofsson, A. and von Heijne, G. (1999) Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale. J Mol Biol 293 (4) : 807-814.
Cited 0 times , Impact Factor: 5.501
 
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46Elofsson, A. and Sonnhammer, E.L. (1999) A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics 15 (6) : 480-500.
Cited 0 times , Impact Factor: 5.039
 
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47Sander, C., Vriend, G., Bazan, F., Horovitz, A., Nakamura, H., Ribas, L., Finkelstein, A.V., Lockhart, A., Merkl, R., Perry, L.J. and others (1992) Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida. Proteins 12 (2) : 105-110.
Cited 0 times , Impact Factor: 3.354
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48Asa Bjorklund, Anna Thoren, Gunnar von Heijne and Arne Elofsson (2006) The use of Phylogenetic profils for Gene Predictions Revisited Current Genomics 7 (2) : 79-86.
Cited 0 times , Impact Factor: 0.573
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49Elofsson, A. and von Heijne, G. (2007) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76: 125-140.
Cited 0 times , Impact Factor: 31.19
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50Wallner, B., Larsson, P. and Elofsson, A. (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res 35 (suppl_2) : W369-W374.
Cited 0 times , Impact Factor: 6.954
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51Ekman, D., Bjorklund, A.K. and Elofsson, A. (2007) Quantification of the elevated rate of domain rearrangements in metazoa. J Mol Biol 372 (5) : 1337-1348.
Cited 0 times , Impact Factor: 5.501
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52Wallner, B. and Elofsson, A. (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69 (S8) : 184-193.
Cited 0 times , Impact Factor: 3.354
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53Bernsel, A., Viklund, H. and Elofsson, A. (2008) Remote homology detection of integral membrane proteins using conserved sequence features. Proteins 71 (3) : 1387-1399.
Cited 0 times , Impact Factor: 3.354
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54Larsson, P., Wallner, B., Lindahl, E. and Elofsson, A. (2008) Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci 17 (6) : 990-1002.
Cited 0 times , Impact Factor: 3.135
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55Bernsel, A., Viklund, H., Falk, J., Lindahl, E., von Heijne, G. and Elofsson, A. (2008) Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A 105 (20) : 7177-7181.
Cited 0 times , Impact Factor: 9.598
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56Kauko, A., Illergard, K. and Elofsson, A. (2008) Coils in the membrane core are conserved and functionally important. J Mol Biol 380 (1) : 170-180.
Cited 0 times , Impact Factor: 5.501
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57Viklund, H. and Elofsson, A. (2008) OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics 24 (15) : 1662-1668.
Cited 0 times , Impact Factor: 5.039
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58Hughes, T., Ekman, D., Ardawatia, H., Elofsson, A. and Liberles, D.A. (2007) Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol 8 (5) : 213.
Cited 0 times , Impact Factor: 10.3
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59Elofsson, A., Fischer, D., Rice, D.W., Le Grand, S.M. and Eisenberg, D. (1996) A study of combined structure/sequence profiles. Fold Des 1 (6) : 451-461.
Cited 0 times , Impact Factor: -1
 
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60Garemyr, R. and Elofsson, A. (1999) Study of the electrostatics treatment in molecular dynamics simulations. Proteins 37 (3) : 417-428.
Cited 0 times , Impact Factor: 3.354
 
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61Siew, N., Elofsson, A., Rychlewski, L. and Fischer, D. (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 16 (9) : 776-785.
Cited 0 times , Impact Factor: 5.039
 
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62Lindahl, E. and Elofsson, A. (2000) Identification of related proteins on family, superfamily and fold level. J Mol Biol 295 (3) : 613-625.
Cited 0 times , Impact Factor: 5.501
 
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63Hargbo, J. and Elofsson, A. (1999) Hidden Markov models that use predicted secondary structures for fold recognition. Proteins 36 (1) : 68-76.
Cited 0 times , Impact Factor: 3.354
 
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64Elofsson, A., Nilsson, L. and Rigler, R. (1990) Studies on somatostatin with time-resolved spectroscopy and molecular dynamics simulations. Int J Pept Protein Res 36 (3) : 297-301.
Cited 0 times , Impact Factor: 2.269
 
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65Fischer, D., Barret, C., Bryson, K., Elofsson, A., Godzik, A., Jones, D., Karplus, K.J., Kelley, L.A., MacCallum, R.M., Pawowski, K., Rost, B., Rychlewski, L. and Sternberg, M. (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins Suppl 3: 209-217.
Cited 0 times , Impact Factor: 3.354
 
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66Elofsson, A. and Nilsson, L. (1993) How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. J Mol Biol 233 (4) : 766-780.
Cited 0 times , Impact Factor: 5.501
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67Zhang, X.P., Elofsson, A., Andreu, D. and Glaser, E. (1999) Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70. J Mol Biol 288 (1) : 177-190.
Cited 0 times , Impact Factor: 5.501
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68Fischer, D., Elofsson, A. and Rychlewski, L. (2000) The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-a-vis human teams in the protein structure prediction experiment CAFASP2. Protein Eng 13 (10) : 667-670.
Cited 0 times , Impact Factor: 2.662
 
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69Elofsson, A., Rigler, R., Nilsson, L., Roslund, J., Krause, G. and Holmgren, A. (1991) 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 Biochemistry 30 (40) : 9648-9656.
Cited 0 times , Impact Factor: 3.368
 
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70Eriksson, O., Xhou, Y. and Elofsson, A. (2001) Side chain-positioning as an integer programming problem. WABI 1: 1-1.
Cited 0 times , Impact Factor: -1
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71LeGrand, S.M., Elofsson A. and Eisenberg, D. (1994) The Effect of a Distance Cutoff on the Performance of the Distance Matrix Error when Used as a Potential Function to Drive Conformational Search In: Distance-based Approaches to Protein Structure Determination I 2: 1-1.
Cited 0 times , Impact Factor: 2.269
 
72Elofsson, A (1997) Recent advances in how to test knowledge based energy functions for protein folding studies Recent Research Developments in Physical Chemistry 1: 1-1.
Cited 0 times , Impact Factor: -1
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73Zhang, X.-P., Elofsson, A. and Glaser, E. (1998) Interaction of mt-HSP70 with mitochondrial presequences Plant Mitochondria: From gene to Function (Moller, I.M., Gardeström, P., Glimelius, K. and Glaser, E., eds) 1: 1-1.
Cited 0 times , Impact Factor: 2.269
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74Fang, H., Wallner, B. Lundström, J., von Wowern, C. and Elofsson, A. (2001) Improved fold recognition by using the Pcons consensus approach Chapter in “Protein structure prediction:Bioinformatic approach” IUL biotechnology Series, La Jolla, 1: 397-41.
Cited 0 times , Impact Factor: 2.269
 
75Wallner, B., and Elofsson, A. (2008) Prediction of global and local model qualities using MQAPs Eds Bujnicki 1: 1-1.
Cited 0 times , Impact Factor: 2.269
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76Moore, A.D., Bjorklund, A.K., Ekman, D., Bornberg-Bauer, E. and Elofsson, A. (2008) Arrangements in the modular evolution of proteins. Trends Biochem Sci 33 (9) : 444-451.
Cited 0 times , Impact Factor: 14.994
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77Emanuelsson, O., Elofsson, A., von Heijne, G. and Cristobal, S. (2003) In silico prediction of the peroxisomal proteome in fungi, plants and animals. J Mol Biol 330 (2) : 443-456.
Cited 0 times , Impact Factor: 5.501
 
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78Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Sci 10 (2) : 352-361.
Cited 0 times , Impact Factor: 3.135
 
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79Granseth, E., von Heijne, G. and Elofsson, A. (2005) A study of the membrane-water interface region of membrane proteins. J Mol Biol 346 (1) : 377-385.
Cited 0 times , Impact Factor: 5.501
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80 Elofsson, A., Le Grand, S.M. and Eisenberg, D. (1995) Local moves: an efficient algorithm for simulation of protein folding Proteins 23 (1) : 73-82.
Cited 0 times , Impact Factor: 3.354
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81Ohlson, T., Wallner, B. and Elofsson, A. (2004) Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 57 (1) : 188-197.
Cited 0 times , Impact Factor: 3.354
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82Bjorklund, A.K., Light, S., Hedin, L. and Elofsson, A. (2008) Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics 8 (22) : 4657-4667.
Cited 0 times , Impact Factor: 5.479
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83Viklund, H., Bernsel, A., Skwark, M. and Elofsson, A. (2008) SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics 24 (24) : 2928-2929.
Cited 0 times , Impact Factor: 5.039
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84Wallner, B. and Elofsson, A. (2005) Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 21 (23) : 4248-4254.
Cited 0 times , Impact Factor: 5.039
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85Rigler, R., Wennerberg, A. B. A., Cooke, R. M., Elofsson, A. , Nilsson, L., Vogel, H., Holley, L. H., Carlquist, M., Langel, U., Bartfai, T., and Campbell, I. (1991) On the solution structure of Galanin Galanin : 1-1.
Cited 0 times , Impact Factor: 0
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86Ohlson, T., Aggarwal, V., Elofsson, A. and MacCallum, R.M. (2006) Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. BMC Bioinformatics 7: 357.
Cited 0 times , Impact Factor: 3.493
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87Michino, M., Abola, E., Brooks, 3rd, C.L., Dixon, J.S., Moult, J. and Stevens, R.C. (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov 8 (6) : 455-463.
Cited 0 times , Impact Factor: 23.308
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88Illergard, K., Ardell, D.H. and Elofsson, A. (2009) Structure is three to ten times more conserved than sequence-A study of structural response in protein cores. Proteins 77 (3) : 499-508.
Cited 0 times , Impact Factor: 3.354
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89Bernsel, A., Viklund, H., Hennerdal, A. and Elofsson, A. (2009) TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res 37 (Web Server issue) : W465-8.
Cited 0 times , Impact Factor: 6.954
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90Larsson, P., Skwark, M.J., Wallner, B. and Elofsson, A. (2009) Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins 77 (S9) : 167-172.
Cited 0 times , Impact Factor: 3.354
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91Ekman, D. and Elofsson, A. (2010) Identifying and Quantifying Orphan Protein Sequences in Fungi. J Mol Biol 396 (2) : 396-405.
Cited 0 times , Impact Factor: 5.501
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92Hedin, L.E., Ojemalm, K., Bernsel, A., Hennerdal, A., Illergard, K., Enquist, K., Kauko, A., Cristobal, S., von Heijne, G., Lerch-Bader, M., Nilsson, I. and Elofsson, A. (2010) Membrane Insertion of Marginally Hydrophobic Transmembrane Helices Depends on Sequence Context. J Mol Biol 396 (1) : 221-229.
Cited 0 times , Impact Factor: 5.501
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93Kauko, A., Hedin, L.E., Thebaud, E., Cristobal, S., Elofsson, A. and von Heijne, G. (2010) Repositioning of Transmembrane alpha-Helices during Membrane Protein Folding. J Mol Biol 397 (1) : 190-201.
Cited 0 times , Impact Factor: 5.501
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94Illergard, K., Kauko, A. and Elofsson, A. (2011) Why are polar residues within the membrane core evolutionary conserved? Proteins 79 (1) : 79-91.
Cited 0 times , Impact Factor: 3.354
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95Illergard, K., Callegari, S. and Elofsson, A. (2010) MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane. BMC Bioinformatics 11 (1) : 333.
Cited 0 times , Impact Factor: 3.493
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96Bjorklund, A.K., Light, S., Sagit, R. and Elofsson, A. (2010) Nebulin: A Study of Protein Repeat Evolution. J Mol Biol 402 (1) : 38-51.
Cited 0 times , Impact Factor: 5.501
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97Runesson, J., Sollenberg, U.E., Jurkowski, W., Yazdi, S., Eriksson, E.E., Elofsson, A. and Langel, U. (2010) Determining receptor-ligand interaction of human galanin receptor type 3. Neurochem Int 57 (7) : 804-811.
Cited 0 times , Impact Factor: 2.175
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98Lima, M.F., Eloy, N.B., Pegoraro, C., Sagit, R., Rojas, C., Bretz, T., Vargas, L., Elofsson, A., Oliveira, A.C., Hemerly, A.S. and Ferreira, P.C. (2010) Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. BMC Plant Biol 10 (1) : 254.
Cited 0 times , Impact Factor: 3.232
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99Hennerdal, A., Falk, J., Lindahl, E. and Elofsson, A. (2010) Internal duplications in alpha-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Sci 19 (12) : 2305-2318.
Cited 0 times , Impact Factor: 3.135
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100Larsson, P., Skwark, M.J., Wallner, B. and Elofsson, A. (2011) Improved predictions by Pcons.net using multiple templates. Bioinformatics 27 (3) : 426-427.
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101Basmarke-Wehelie, R., Sjolinder, H., Jurkowski, W., Elofsson, A., Arnqvist, A., Engstrand, L., Hagner, M., Wallin, E., Guan, N., Kuranasekera, H., Aro, H. and Jonsson, A.B. (2011) The Complement Regulator CD46 Is Bactericidal to Helicobacter pylori and Blocks Urease Activity. Gastroenterology 141 (3) : 918-928.
Cited 0 times , Impact Factor: 12.182
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102Hennerdal, A. and Elofsson, A. (2011) Rapid membrane protein topology prediction. Bioinformatics 27 (9) : 1322-1323.
Cited 0 times , Impact Factor: 5.039
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103Shu, N. and Elofsson, A. (2011) KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics 27 (12) : 1702-1703.
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104Contreras, F.X., Ernst, A.M., Haberkant, P., Bjorkholm, P., Lindahl, E., Gonen, B., Tischer, C., Elofsson, A., von Heijne, G., Thiele, C., Pepperkok, R., Wieland, F. and Brugger, B. (2012) Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature 481 (7382) : 525-529.
Cited 0 times , Impact Factor: 28.751
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105Hayat, S. and Elofsson, A. (2012) BOCTOPUS: improved topology prediction of transmembrane beta barrel proteins. Bioinformatics 28 (4) : 516-522.
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106Norholm, M.H., Light, S., Virkki, M.T., Elofsson, A., von Heijne, G. and Daley, D.O. (2012) Manipulating the genetic code for membrane protein production: what have we learnt so far? Biochim Biophys Acta 1818 (4) : 1091-1096.
Cited 0 times , Impact Factor: 2.59
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107Light, S., Sagit, R., Ithychanda, S.S., Qin, J. and Elofsson, A. (2012) The evolution of filamin-a protein domain repeat perspective. J Struct Biol 179 (3) : 289-298.
Cited 0 times , Impact Factor: 2.986
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108Liberles, D.A., Teichmann, S.A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L.J., de Koning, A.P., Dokholyan, N.V., Echave, J., Elofsson, A., Gerloff, D.L., Goldstein, R.A., Grahnen, J.A., Holder, M.T., Lakner, C., Lartillot, N., Lovell, S.C., Naylor, G., Perica, T., Pollock, D.D., Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjolander, K., Sunyaev, S., Teufel, A.I., Thorne, J.L., Thornton, J.W., Weinreich, D.M. and Whelan, S. (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 21 (6) : 769-785.
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109Hayat, S. and Elofsson, A. (2012) Ranking models of transmembrane beta-barrel proteins using Z-coordinate predictions. Bioinformatics 28 (12) : i90-6.
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110Tsirigos, K.D., Hennerdal, A., Kall, L. and Elofsson, A. (2012) A guideline to proteome-wide alpha-helical membrane protein topology predictions. Proteomics 12 (14) : 2282-2294.
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111Light, S., Sagit, R., Ekman, D. and Elofsson, A. (2013) Long indels are disordered: A study of disorder and indels in homologous eukaryotic proteins. Biochim Biophys Acta 1834 (5) : 890-897.
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112Bano-Polo, M., Martinez-Gil, L., Wallner, B., Nieva, J.L., Elofsson, A. and Mingarro, I. (2013) Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. J Mol Biol 425 (4) : 830-840.
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113Jurkowski, W., Yazdi, S. and Elofsson, A. (2013) Ligand binding properties of human galanin receptors. Mol Membr Biol 30 (2) : 206-216.
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114Imai, K., Hayat, S., Sakiyama, N., Fujita, N., Tomii, K., Elofsson, A. and Horton, P. (2013) Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods Mol Biol 939: 115-140.
Cited 0 times , Impact Factor: 3.667
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115Bendz, M., Skwark, M., Nilsson, D., Granholm, V., Cristobal, S., Kall, L. and Elofsson, A. (2013) Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics 13 (9) : 1467-1480.
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116Light, S. and Elofsson, A. (2013) The impact of splicing on protein domain architecture. Curr Opin Struct Biol 23 (3) : 451-458.
Cited 0 times , Impact Factor: 10.15
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117Skwark, M.J., Abdel-Rehim, A. and Elofsson, A. (2013) PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics 29 (14) : 1815-1816.
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118Skwark, M.J. and Elofsson, A. (2013) PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. Bioinformatics 29 (14) : 1817-1818.
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119Light, S., Sagit, R., Sachenkova, O., Ekman, D. and Elofsson, A. (2013) Protein expansion is primarily due to indels in intrinsically disordered regions. Mol Biol Evol 30 (12) : 2645-2653.
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120Peters, C. and Elofsson, A. (2014) Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins 82 (9) : 2190-2198.
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121Virkki, M.T., Agrawal, N., Edsbacker, E., Cristobal, S., Elofsson, A. and Kauko, A. (2014) Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Sci 23 (7) : 981-992.
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122Virkki, M., Boekel, C., Illergard, K., Peters, C., Shu, N., Tsirigos, K.D., Elofsson, A., von Heijne, G. and Nilsson, I. (2014) Large tilts in transmembrane helices can be induced during tertiary structure formation. J Mol Biol 426 (13) : 2529-2538.
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123Light, S., Basile, W. and Elofsson, A. (2014) Orphans and new gene origination, a structural and evolutionary perspective. Curr Opin Struct Biol 26: 73-83.
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124Virkki, M.T., Peters, C., Nilsson, D., Sorensen, T., Cristobal, S., Wallner, B. and Elofsson, A. (2014) The positive inside rule is stronger when followed by a transmembrane helix. J Mol Biol 426 (16) : 2982-2991.
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125Michel, M., Hayat, S., Skwark, M.J., Sander, C., Marks, D.S. and Elofsson, A. (2014) PconsFold: improved contact predictions improve protein models. Bioinformatics 30 (17) : i482-8.
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126Skwark, M.J., Raimondi, D., Michel, M. and Elofsson, A. (2014) Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput Biol 10 (11) : e1003889.
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127Hayat, S., Sander, C., Marks, D.S. and Elofsson, A. (2015) All-atom 3D structure prediction of transmembrane beta-barrel proteins from sequences. Proc Natl Acad Sci U S A 112 (17) : 5413-5418.
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128Mirzadeh, K., Martinez, V., Toddo, S., Guntur, S., Herrgard, M.J., Elofsson, A., Norholm, M.H. and Daley, D.O. (2015) Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction. ACS Synth Biol 4 (9) : 959-965.
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129De Marothy, M.T. and Elofsson, A. (2015) Marginally hydrophobic transmembrane alpha-helices shaping membrane protein folding. Protein Sci 24 (7) : 1057-1074.
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130Tsirigos, K.D., Peters, C., Shu, N., Kall, L. and Elofsson, A. (2015) The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res 43 (W1) : W401-7.
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131Shiota, T., Imai, K., Qiu, J., Hewitt, V.L., Tan, K., Shen, H.H., Sakiyama, N., Fukasawa, Y., Hayat, S., Kamiya, M., Elofsson, A., Tomii, K., Horton, P., Wiedemann, N., Pfanner, N., Lithgow, T. and Endo, T. (2015) Molecular architecture of the active mitochondrial protein gate. Science 349 (6255) : 1544-1548.
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132Peters, C., Tsirigos, K.D., Shu, N. and Elofsson, A. (2016) Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics 32 (8) : 1158-1162.
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133Hayat, S., Peters, C., Shu, N., Tsirigos, K.D. and Elofsson, A. (2016) Inclusion of dyad-repeat pattern improves topology prediction of transmembrane beta-barrel proteins. Bioinformatics 32 (10) : 1571-1573.
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134Lamb, J., Jarmolinska, A.I., Michel, M., Menendez-Hurtado, D., Sulkowska, J.I. and Elofsson, A. (2019) PconsFam: An Interactive Database of Structure Predictions of Pfam Families. J Mol Biol 431 (13) : 2442-2448.
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135Michel, M., Menendez Hurtado, D. and Elofsson, A. (2019) PconsC4: fast, accurate and hassle-free contact predictions. Bioinformatics 35 (15) : 2677-2679.
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136Bassot, C., Menendez Hurtado, D. and Elofsson, A. (2019) Using PconsC4 and PconsFold2 to Predict Protein Structure. Curr Protoc Bioinformatics 66 (1) : e75.
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137Tsirigos, K.D., Elofsson, A. and Bagos, P.G. (2016) PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. Bioinformatics 32 (17) : i665-i671.
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138Uziela, K., Shu, N., Wallner, B. and Elofsson, A. (2016) ProQ3: Improved model quality assessments using Rosetta energy terms. Sci Rep 6: 33509.
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139Basile, W., Sachenkova, O., Light, S. and Elofsson, A. (2017) High GC content causes orphan proteins to be intrinsically disordered. PLoS Comput Biol 13 (3) : e1005375.
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140Dimou, N.L., Tsirigos, K.D., Elofsson, A. and Bagos, P.G. (2017) GWAR: robust analysis and meta-analysis of genome-wide association studies. Bioinformatics 33 (10) : 1521-1527.
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141Salvatore, M., Warholm, P., Shu, N., Basile, W. and Elofsson, A. (2017) SubCons: a new ensemble method for improved human subcellular localization predictions. Bioinformatics 33 (16) : 2464-2470.
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142Uziela, K., Menendez Hurtado, D., Shu, N., Wallner, B. and Elofsson, A. (2017) ProQ3D: improved model quality assessments using deep learning. Bioinformatics 33 (10) : 1578-1580.
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143Michel, M., Skwark, M.J., Menendez Hurtado, D., Ekeberg, M. and Elofsson, A. (2017) Predicting accurate contacts in thousands of Pfam domain families using PconsC3. Bioinformatics 33 (18) : 2859-2866.
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144Michel, M., Menendez Hurtado, D., Uziela, K. and Elofsson, A. (2017) Large-scale structure prediction by improved contact predictions and model quality assessment. Bioinformatics 33 (14) : i23-i29.
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145Salvatore, M., Shu, N. and Elofsson, A. (2018) The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction. Protein Sci 27 (1) : 195-201.
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146Elofsson, A., Joo, K., Keasar, C., Lee, J., Maghrabi, A.H.A., Manavalan, B., McGuffin, L.J., Menendez Hurtado, D., Mirabello, C., Pilstal, R., Sidi, T., Uziela, K. and Wallner, B. (2018) Methods for estimation of model accuracy in CASP12. Proteins 86 Suppl 1: 361-373.
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147Uziela, K., Menendez Hurtado, D., Shu, N., Wallner, B. and Elofsson, A. (2018) Improved protein model quality assessments by changing the target function. Proteins 86 (6) : 654-663.
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148Tsirigos, K.D., Govindarajan, S., Bassot, C., Vastermark, A., Lamb, J., Shu, N. and Elofsson, A. (2018) Topology of membrane proteins-predictions, limitations and variations. Curr Opin Struct Biol 50: 9-17.
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149Cheng, J., Choe, M.H., Elofsson, A., Han, K.S., Hou, J., Maghrabi, A.H.A., McGuffin, L.J., Menendez-Hurtado, D., Olechnovic, K., Schwede, T., Studer, G., Uziela, K., Venclovas, C. and Wallner, B. (2019) Estimation of model accuracy in CASP13. Proteins 87 (12) : 1361-1377.
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150Basile, W., Salvatore, M., Bassot, C. and Elofsson, A. (2019) Why do eukaryotic proteins contain more intrinsically disordered regions? PLoS Comput Biol 15 (7) : e1007186.
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151Elofsson, A., Hess, B., Lindahl, E., Onufriev, A., van der Spoel, D. and Wallqvist, A. (2019) Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput Biol 15 (1) : e1006649.
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152Ndi, M., Masuyer, G., Dawitz, H., Carlstrom, A., Michel, M., Elofsson, A., Rapp, M., Stenmark, P. and Ott, M. (2019) Structural basis for the interaction of the chaperone Cbp3 with newly synthesized cytochrome b during mitochondrial respiratory chain assembly. J Biol Chem 294 (45) : 16663-16671.
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153Allison, T.M., Degiacomi, M.T., Marklund, E.G., Jovine, L., Elofsson, A., Benesch, J.L.P. and Landreh, M. (2022) Complementing machine learning-based structure predictions with native mass spectrometry. Protein Sci 31 (6) : e4333.
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154Pozzati, G., Kundrotas, P. and Elofsson, A. (2022) Scoring of protein-protein docking models utilizing predicted interface residues. Proteins 90 (7) : 1493-1505.
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155Hatos, A., Hajdu-Soltesz, B., Monzon, A.M., Palopoli, N., Alvarez, L., Aykac-Fas, B., Bassot, C., Benitez, G.I., Bevilacqua, M., Chasapi, A., Chemes, L., Davey, N.E., Davidovic, R., Dunker, A.K., Elofsson, A., Gobeill, J., Foutel, N.S.G., Sudha, G., Guharoy, M., Horvath, T., Iglesias, V., Kajava, A.V., Kovacs, O.P., Lamb, J., Lambrughi, M., Lazar, T., Leclercq, J.Y., Leonardi, E., Macedo-Ribeiro, S., Macossay-Castillo, M., Maiani, E., Manso, J.A., Marino-Buslje, C., Martinez-Perez, E., Meszaros, B., Micetic, I., Minervini, G., Murvai, N., Necci, M., Ouzounis, C.A., Pajkos, M., Paladin, L., Pancsa, R., Papaleo, E., Parisi, G., Pasche, E., Barbosa Pereira, P.J., Promponas, V.J., Pujols, J., Quaglia, F., Ruch, P., Salvatore, M., Schad, E., Szabo, B., Szaniszlo, T., Tamana, S., Tantos, A., Veljkovic, N., Ventura, S., Vranken, W., Dosztanyi, Z., Tompa, P., Tosatto, S.C.E. and Piovesan, D. (2020) DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res 48 (D1) : D269-D276.
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156Bryant, P. and Elofsson, A. (2020) Decomposing Structural Response Due to Sequence Changes in Protein Domains with Machine Learning. J Mol Biol 432 (16) : 4435-4446.
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157Li, Z., Lin, Y., Elofsson, A. and Yao, Y. (2020) Protein Contact Map Prediction Based on ResNet and DenseNet. Biomed Res Int 2020: 7584968.
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158Bryant, P., Pozzati, G. and Elofsson, A. (2022) Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun 13 (1) : 1265.
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159Sudha, G., Bassot, C., Lamb, J., Shu, N., Huang, Y. and Elofsson, A. (2021) The evolutionary history of topological variations in the CPA/AT transporters. PLoS Comput Biol 17 (8) : e1009278.
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160Laine, E., Eismann, S., Elofsson, A. and Grudinin, S. (2021) Protein sequence-to-structure learning: Is this the end(-to-end revolution)? Proteins 89 (12) : 1770-1786.
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161Duart, G., Lamb, J., Ortiz-Mateu, J., Elofsson, A. and Mingarro, I. (2022) Intra-Helical Salt Bridge Contribution to Membrane Protein Insertion. J Mol Biol 434 (5) : 167467.
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162Quaglia, F., Meszaros, B., Salladini, E., Hatos, A., Pancsa, R., Chemes, L.B., Pajkos, M., Lazar, T., Pena-Diaz, S., Santos, J., Acs, V., Farahi, N., Ficho, E., Aspromonte, M.C., Bassot, C., Chasapi, A., Davey, N.E., Davidovic, R., Dobson, L., Elofsson, A., Erdos, G., Gaudet, P., Giglio, M., Glavina, J., Iserte, J., Iglesias, V., Kalman, Z., Lambrughi, M., Leonardi, E., Longhi, S., Macedo-Ribeiro, S., Maiani, E., Marchetti, J., Marino-Buslje, C., Meszaros, A., Monzon, A.M., Minervini, G., Nadendla, S., Nilsson, J.F., Novotny, M., Ouzounis, C.A., Palopoli, N., Papaleo, E., Pereira, P.J.B., Pozzati, G., Promponas, V.J., Pujols, J., Rocha, A.C.S., Salas, M., Sawicki, L.R., Schad, E., Shenoy, A., Szaniszlo, T., Tsirigos, K.D., Veljkovic, N., Parisi, G., Ventura, S., Dosztanyi, Z., Tompa, P., Tosatto, S.C.E. and Piovesan, D. (2022) DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res 50 (D1) : D480-D487.
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163Bryant, P., Pozzati, G. and Elofsson, A. (2022) Author Correction: Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun 13 (1) : 1694.
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164Bryant, P. and Elofsson, A. (2022) The relationship between ageing and changes in the human blood and brain methylomes. NAR Genom Bioinform 4 (1) : lqac001.
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165Li, Z., Jiang, K., Qin, S., Zhong, Y. and Elofsson, A. (2021) GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction. PLoS Comput Biol 17 (6) : e1009048.
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