Articles ordered by citations | | | | | | | | |
| 1 | Tsirigos, 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.
Cited 898 times , Impact Factor: 6.954
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| 2 | Bryant, P., Pozzati, G. and Elofsson, A. (2022) Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun 13 (1) : 1265.
Cited 629 times , Impact Factor: 14.92
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| 3 | Hatos, 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.
Cited 249 times , Impact Factor: 6.954
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| 4 | Shiota, 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.
Cited 239 times , Impact Factor: 26.372
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| 5 | Uziela, 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.
Cited 178 times , Impact Factor: 5.039
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| 6 | Burke, D.F., Bryant, P., Barrio-Hernandez, I., Memon, D., Pozzati, G., Shenoy, A., Zhu, W., Dunham, A.S., Albanese, P., Keller, A., Scheltema, R.A., Bruce, J.E., Leitner, A., Kundrotas, P., Beltrao, P. and Elofsson, A. (2023) Towards a structurally resolved human protein interaction network. Nat Struct Mol Biol 30 (2) : 216-225.
Cited 156 times , Impact Factor: 11.085
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| 7 | Bryant, 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 138 times , Impact Factor: 14.92
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| 8 | Quaglia, 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.
Cited 137 times , Impact Factor: 6.954
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| 9 | Baldassarre, 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 114 times , Impact Factor: 5.039
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| 10 | Fischer, 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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| 11 | Uziela, K., Shu, N., Wallner, B. and Elofsson, A. (2016) ProQ3: Improved model quality assessments using Rosetta energy terms. Sci Rep 6: 33509.
Cited 110 times , Impact Factor: 0
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| 12 | Cheng, 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.
Cited 93 times , Impact Factor: 3.354
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| 13 | Tsirigos, 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.
Cited 88 times , Impact Factor: 5.039
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| 14 | Hayat, 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.
Cited 87 times , Impact Factor: 5.039
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| 15 | Basile, W., Salvatore, M., Bassot, C. and Elofsson, A. (2019) Why do eukaryotic proteins contain more intrinsically disordered regions? PLoS Comput Biol 15 (7) : e1007186.
Cited 85 times , Impact Factor: 6.236
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| 16 | Michel, M., Menendez Hurtado, D. and Elofsson, A. (2019) PconsC4: fast, accurate and hassle-free contact predictions. Bioinformatics 35 (15) : 2677-2679.
Cited 81 times , Impact Factor: 5.039
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| 17 | Mirzadeh, 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.
Cited 69 times , Impact Factor: 4.978
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| 18 | Basile, 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.
Cited 68 times , Impact Factor: 6.236
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| 19 | Hayat, 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.
Cited 64 times , Impact Factor: 9.598
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| 20 | Bryant, P. and Elofsson, A. (2020) Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries. PeerJ 8: e9879.
Cited 64 times , Impact Factor: 2.984
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| 21 | Peters, C., Tsirigos, K.D., Shu, N. and Elofsson, A. (2016) Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics 32 (8) : 1158-1162.
Cited 58 times , Impact Factor: 5.039
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| 22 | Michel, 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.
Cited 48 times , Impact Factor: 5.039
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| 23 | De Marothy, M.T. and Elofsson, A. (2015) Marginally hydrophobic transmembrane alpha-helices shaping membrane protein folding. Protein Sci 24 (7) : 1057-1074.
Cited 44 times , Impact Factor: 3.135
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| 24 | Li, Z., Lin, Y., Elofsson, A. and Yao, Y. (2020) Protein Contact Map Prediction Based on ResNet and DenseNet. Biomed Res Int 2020: 7584968.
Cited 38 times , Impact Factor: 1
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| 25 | Laine, 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.
Cited 38 times , Impact Factor: 3.354
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| 26 | Michel, 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.
Cited 36 times , Impact Factor: 5.039
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| 27 | Elofsson, 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.
Cited 36 times , Impact Factor: 6.236
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| 28 | Salvatore, 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.
Cited 34 times , Impact Factor: 5.039
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| 29 | Elofsson, 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.
Cited 34 times , Impact Factor: 3.354
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| 30 | Tsirigos, 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.
Cited 34 times , Impact Factor: 10.15
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| 31 | Light, S., Basile, W. and Elofsson, A. (2014) Orphans and new gene origination, a structural and evolutionary perspective. Curr Opin Struct Biol 26: 73-83.
Cited 31 times , Impact Factor: 10.15
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| 32 | Virkki, 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.
Cited 24 times , Impact Factor: 3.135
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| 33 | Peters, C. and Elofsson, A. (2014) Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins 82 (9) : 2190-2198.
Cited 23 times , Impact Factor: 3.354
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| 34 | Uziela, 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.
Cited 21 times , Impact Factor: 3.354
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| 35 | Li, 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.
Cited 21 times , Impact Factor: 6.236
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| 36 | Hedin, 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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| 37 | Virkki, 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.
Cited 18 times , Impact Factor: 5.501
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| 38 | Lamb, 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.
Cited 16 times , Impact Factor: 5.501
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| 39 | Salvatore, 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.
Cited 15 times , Impact Factor: 3.135
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| 40 | Allison, 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.
Cited 14 times , Impact Factor: 3.135
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| 41 | Ernits, K., Saha, C.K., Brodiazhenko, T., Chouhan, B., Shenoy, A., Buttress, J.A., Duque-Pedraza, J.J., Bojar, V., Nakamoto, J.A., Kurata, T., Egorov, A.A., Shyrokova, L., Johansson, M.J.O., Mets, T., Rustamova, A., Dzigurski, J., Tenson, T., Garcia-Pino, A., Strahl, H., Elofsson, A., Hauryliuk, V. and Atkinson, G.C. (2023) The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems. Proc Natl Acad Sci U S A 120 (33) : e2305393120.
Cited 14 times , Impact Factor: 9.598
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| 42 | Dimou, 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.
Cited 13 times , Impact Factor: 5.039
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| 43 | Virkki, 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.
Cited 12 times , Impact Factor: 5.501
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| 44 | Ndi, 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.
Cited 9 times , Impact Factor: 5.581
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| 45 | Osterlund, 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 9 times , Impact Factor: 13.156
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| 46 | Elofsson, 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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| 47 | Dahl, L., Kotliar, I.B., Bendes, A., Dodig-Crnkovic, T., Fromm, S., Elofsson, A., Uhlen, M., Sakmar, T.P. and Schwenk, J.M. (2023) Multiplexed selectivity screening of anti-GPCR antibodies. Sci Adv 9 (18) : eadf9297.
Cited 8 times , Impact Factor: 0
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| 48 | Bassot, C., Menendez Hurtado, D. and Elofsson, A. (2019) Using PconsC4 and PconsFold2 to Predict Protein Structure. Curr Protoc Bioinformatics 66 (1) : e75.
Cited 7 times , Impact Factor: 0
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| 49 | Saluri, M., Leppert, A., Gese, G.V., Sahin, C., Lama, D., Kaldmae, M., Chen, G., Elofsson, A., Allison, T.M., Arsenian-Henriksson, M., Johansson, J., Lane, D.P., Hallberg, B.M. and Landreh, M. (2023) A "grappling hook" interaction connects self-assembly and chaperone activity of Nucleophosmin 1. PNAS Nexus 2 (2) : pgac303.
Cited 6 times , Impact Factor: 9.598
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| 50 | Duart, 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.
Cited 6 times , Impact Factor: 5.501
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| 51 | Bryant, P. and Elofsson, A. (2023) Peptide binder design with inverse folding and protein structure prediction. Commun Chem 6 (1) : 229.
Cited 6 times , Impact Factor: 0
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| 52 | Pozzati, G., Kundrotas, P. and Elofsson, A. (2022) Scoring of protein-protein docking models utilizing predicted interface residues. Proteins 90 (7) : 1493-1505.
Cited 5 times , Impact Factor: 3.354
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| 53 | Elofsson, 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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| 54 | Elofsson, A. (2021) Toward Characterising the Cellular 3D-Proteome. Front Bioinform 1: 598878.
Cited 3 times , Impact Factor: 0
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| 55 | Sudha, 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.
Cited 3 times , Impact Factor: 6.236
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| 56 | Bryant, P. and Elofsson, A. (2022) The relationship between ageing and changes in the human blood and brain methylomes. NAR Genom Bioinform 4 (1) : lqac001.
Cited 3 times , Impact Factor: 1
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| 57 | David 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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| 58 | Kahle, M., Appelgren, S., Elofsson, A., Carroni, M. and Adelroth, P. (2023) Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins. BMC Biol 21 (1) : 47.
Cited 2 times , Impact Factor: 5.059
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| 59 | Bryant, 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.
Cited 1 times , Impact Factor: 5.501
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| 60 | Cristobal, 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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| 61 | Elofsson, 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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| 62 | Milchert, 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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| 63 | Hedman, 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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| 64 | Bujnicki, 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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| 65 | Bujnicki, 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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| 66 | Berglund, 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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| 67 | Ginalski, 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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| 68 | Donnes, 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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| 69 | Ohlson, 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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| 70 | Elofsson, 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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| 71 | Bjorklund, 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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| 72 | Lundstrom, 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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| 73 | Wallner, 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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| 74 | Light, 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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| 75 | Wallner, 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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| 76 | Fischer, 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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| 77 | Viklund, 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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| 78 | Rychlewski, 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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| 79 | Wallner, 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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| 80 | Wallner, 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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| 81 | Ekman, 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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| 82 | Ekman, 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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| 83 | Bjorklund, A.K., Ekman, D. and Elofsson, A. (2006) Expansion of Protein Domain Repeats. PLoS Comput Biol 2 (8) : e114.
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| 84 | Granseth, 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.
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| 85 | Viklund, 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.
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| 86 | Wallner, B. and Elofsson, A. (2006) Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 15 (4) : 900-913.
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| 87 | Amico, 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.
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| 88 | Papaloukas, 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.
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| 89 | Fischer, 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.
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| 90 | Seshadri, 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.
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| 91 | Wallin, 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.
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| 92 | Mingarro, I., Elofsson, A. and von Heijne, G. (1997) Helix-helix packing in a membrane-like environment. J Mol Biol 272 (4) : 633-641.
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| 93 | Cserzo, 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.
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| 94 | Monne, 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.
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| 95 | Elofsson, 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.
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| 96 | Sander, 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.
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| 97 | Asa 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.
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| 98 | Elofsson, A. and von Heijne, G. (2007) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76: 125-140.
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| 99 | Wallner, B., Larsson, P. and Elofsson, A. (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res 35 (suppl_2) : W369-W374.
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| 100 | Ekman, 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.
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| 101 | Wallner, B. and Elofsson, A. (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69 (S8) : 184-193.
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| 102 | Bernsel, A., Viklund, H. and Elofsson, A. (2008) Remote homology detection of integral membrane proteins using conserved sequence features. Proteins 71 (3) : 1387-1399.
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| 103 | Larsson, 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.
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| 104 | Bernsel, 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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| 105 | Kauko, A., Illergard, K. and Elofsson, A. (2008) Coils in the membrane core are conserved and functionally important. J Mol Biol 380 (1) : 170-180.
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| 106 | Viklund, 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.
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| 107 | Hughes, 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.
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| 108 | Elofsson, 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.
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| 109 | Garemyr, R. and Elofsson, A. (1999) Study of the electrostatics treatment in molecular dynamics simulations. Proteins 37 (3) : 417-428.
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| 110 | Siew, 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.
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| 111 | Lindahl, E. and Elofsson, A. (2000) Identification of related proteins on family, superfamily and fold level. J Mol Biol 295 (3) : 613-625.
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| 112 | Hargbo, J. and Elofsson, A. (1999) Hidden Markov models that use predicted secondary structures for fold recognition. Proteins 36 (1) : 68-76.
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| 113 | Elofsson, 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.
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| 114 | Fischer, 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.
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| 115 | Elofsson, 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.
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| 116 | Zhang, 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.
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| 117 | Fischer, 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.
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| 118 | Elofsson, 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.
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| 119 | Eriksson, O., Xhou, Y. and Elofsson, A. (2001) Side chain-positioning as an integer programming problem. WABI 1: 1-1.
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| 120 | LeGrand, 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.
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| 121 | Elofsson, 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.
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| 122 | Zhang, 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.
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| 123 | Fang, 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.
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| 124 | Wallner, 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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| 125 | Moore, 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.
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| 126 | Emanuelsson, 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.
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| 127 | Bujnicki, 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.
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| 128 | Granseth, 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.
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| 129 | 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.
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| 130 | Ohlson, 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.
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| 131 | Bjorklund, 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.
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| 132 | Viklund, 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.
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| 133 | Wallner, B. and Elofsson, A. (2005) Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 21 (23) : 4248-4254.
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| 134 | Rigler, 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.
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| 135 | Ohlson, 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.
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| 136 | Michino, 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.
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| 137 | Illergard, 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.
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| 138 | Bernsel, 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.
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| 139 | Larsson, 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.
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| 140 | Ekman, D. and Elofsson, A. (2010) Identifying and Quantifying Orphan Protein Sequences in Fungi. J Mol Biol 396 (2) : 396-405.
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| 141 | Hedin, 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.
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| 142 | Kauko, 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.
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| 143 | Illergard, 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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| 144 | Illergard, 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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| 145 | Bjorklund, A.K., Light, S., Sagit, R. and Elofsson, A. (2010) Nebulin: A Study of Protein Repeat Evolution. J Mol Biol 402 (1) : 38-51.
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| 146 | Runesson, 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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| 147 | Lima, 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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| 148 | Hennerdal, 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.
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| 149 | Larsson, P., Skwark, M.J., Wallner, B. and Elofsson, A. (2011) Improved predictions by Pcons.net using multiple templates. Bioinformatics 27 (3) : 426-427.
Cited 0 times , Impact Factor: 5.039
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| 150 | Basmarke-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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| 151 | Hennerdal, 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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| 152 | Shu, N. and Elofsson, A. (2011) KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics 27 (12) : 1702-1703.
Cited 0 times , Impact Factor: 5.039
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| 153 | Contreras, 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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| 154 | Hayat, S. and Elofsson, A. (2012) BOCTOPUS: improved topology prediction of transmembrane beta barrel proteins. Bioinformatics 28 (4) : 516-522.
Cited 0 times , Impact Factor: 5.039
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| 155 | Norholm, 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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| 156 | Light, 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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| 157 | Liberles, 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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| 158 | Hayat, 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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| 159 | Tsirigos, 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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| 160 | Light, 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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| 161 | Bano-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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| 162 | Jurkowski, W., Yazdi, S. and Elofsson, A. (2013) Ligand binding properties of human galanin receptors. Mol Membr Biol 30 (2) : 206-216.
Cited 0 times , Impact Factor: 3.87
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| 163 | Imai, 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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| 164 | Bendz, 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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| 165 | Light, 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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| 166 | Skwark, 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.
Cited 0 times , Impact Factor: 5.039
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| 167 | Skwark, 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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| 168 | Light, 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.
Cited 0 times , Impact Factor: 10.353
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| 169 | Michel, 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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| 170 | Skwark, 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.
Cited 0 times , Impact Factor: 6.236
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| 171 | Bryant, P., Pozzati, G. and Elofsson, A. (2022) Author Correction: Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun 13 (1) : 1694.
Cited 0 times , Impact Factor: 14.92
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