| Year |
Citation |
Score |
| 2024 |
Shenoy A, Kalakoti Y, Sundar D, Elofsson A. M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings. Bioinformatics (Oxford, England). 40. PMID 38175787 DOI: 10.1093/bioinformatics/btad782 |
0.312 |
|
| 2023 |
Bryant P, Elofsson A. Peptide binder design with inverse folding and protein structure prediction. Communications Chemistry. 6: 229. PMID 37880344 DOI: 10.1038/s42004-023-01029-7 |
0.302 |
|
| 2023 |
Miguel Monzon A, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Silvina Fornasari M, Parisi G, Piovesan D, Kajava AV, Tosatto SCE. A STRP-ed definition of Structured Tandem Repeats in Proteins. Journal of Structural Biology. 108023. PMID 37652396 DOI: 10.1016/j.jsb.2023.108023 |
0.383 |
|
| 2023 |
Ernits K, Saha CK, Brodiazhenko T, Chouhan B, Shenoy A, Buttress JA, Duque-Pedraza JJ, Bojar V, Nakamoto JA, Kurata T, Egorov AA, Shyrokova L, Johansson MJO, Mets T, Rustamova A, ... ... Elofsson A, et al. The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems. Proceedings of the National Academy of Sciences of the United States of America. 120: e2305393120. PMID 37556498 DOI: 10.1073/pnas.2305393120 |
0.341 |
|
| 2023 |
Elofsson A. Progress at protein structure prediction, as seen in CASP15. Current Opinion in Structural Biology. 80: 102594. PMID 37060758 DOI: 10.1016/j.sbi.2023.102594 |
0.42 |
|
| 2023 |
Burke DF, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham AS, Albanese P, Keller A, Scheltema RA, Bruce JE, Leitner A, Kundrotas P, Beltrao P, ... Elofsson A, et al. Towards a structurally resolved human protein interaction network. Nature Structural & Molecular Biology. PMID 36690744 DOI: 10.1038/s41594-022-00910-8 |
0.345 |
|
| 2022 |
Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, ... ... Elofsson A, et al. A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology. PMID 36344848 DOI: 10.1038/s41594-022-00849-w |
0.352 |
|
| 2022 |
Bryant P, Pozzati G, Elofsson A. Author Correction: Improved prediction of protein-protein interactions using AlphaFold2. Nature Communications. 13: 1694. PMID 35332153 DOI: 10.1038/s41467-022-29480-5 |
0.36 |
|
| 2022 |
Bryant P, Pozzati G, Elofsson A. Improved prediction of protein-protein interactions using AlphaFold2. Nature Communications. 13: 1265. PMID 35273146 DOI: 10.1038/s41467-022-28865-w |
0.415 |
|
| 2022 |
Pozzati G, Kundrotas P, Elofsson A. Scoring of protein-protein docking models utilizing predicted interface residues. Proteins. PMID 35246997 DOI: 10.1002/prot.26330 |
0.321 |
|
| 2022 |
Duart G, Lamb J, Ortiz-Mateu J, Elofsson A, Mingarro I. Intra-Helical Salt Bridge Contribution to Membrane Protein Insertion. Journal of Molecular Biology. 434: 167467. PMID 35093395 DOI: 10.1016/j.jmb.2022.167467 |
0.377 |
|
| 2021 |
Pozzati G, Zhu W, Bassot C, Lamb J, Kundrotas P, Elofsson A. Limits and potential of combined folding and docking. Bioinformatics (Oxford, England). PMID 34788800 DOI: 10.1093/bioinformatics/btab760 |
0.409 |
|
| 2021 |
Bassot C, Elofsson A. Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families. Plos Computational Biology. 17: e1008798. PMID 33857128 DOI: 10.1371/journal.pcbi.1008798 |
0.411 |
|
| 2020 |
Naderi R, Saadati Mollaei H, Elofsson A, Hosseini Ashtiani S. Using Micro- and Macro-Level Network Metrics Unveils Top Communicative Gene Modules in Psoriasis. Genes. 11. PMID 32785106 DOI: 10.3390/Genes11080914 |
0.321 |
|
| 2020 |
Baldassarre F, Hurtado DM, Elofsson A, Azizpour H. GraphQA: Protein Model Quality Assessment using Graph Convolutional Networks. Bioinformatics (Oxford, England). PMID 32780838 DOI: 10.1093/Bioinformatics/Btaa714 |
0.427 |
|
| 2020 |
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000research. 9. PMID 32566135 DOI: 10.12688/F1000Research.20559.1 |
0.305 |
|
| 2020 |
Bryant P, Elofsson A. Decomposing Structural Response Due to Sequence Changes in Protein Domains with Machine Learning. Journal of Molecular Biology. PMID 32485208 DOI: 10.1016/J.Jmb.2020.05.021 |
0.426 |
|
| 2020 |
Li Z, Lin Y, Elofsson A, Yao Y. Protein Contact Map Prediction Based on ResNet and DenseNet. Biomed Research International. 2020: 7584968. PMID 32337273 DOI: 10.1155/2020/7584968 |
0.416 |
|
| 2020 |
Delucchi M, Schaper E, Sachenkova O, Elofsson A, Anisimova M. A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. Genes. 11. PMID 32283633 DOI: 10.3390/Genes11040407 |
0.478 |
|
| 2019 |
Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, et al. An intrinsically disordered proteins community for ELIXIR. F1000research. 8. PMID 31824649 DOI: 10.12688/F1000Research.20136.1 |
0.322 |
|
| 2019 |
Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, et al. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Research. PMID 31713636 DOI: 10.1093/Nar/Gkz975 |
0.353 |
|
| 2019 |
Almagro Armenteros JJ, Salvatore M, Emanuelsson O, Winther O, von Heijne G, Elofsson A, Nielsen H. Detecting sequence signals in targeting peptides using deep learning. Life Science Alliance. 2. PMID 31570514 DOI: 10.26508/lsa.201900429 |
0.53 |
|
| 2019 |
Ndi M, Masuyer G, Dawitz H, Carlström A, Michel M, Elofsson A, Rapp M, Stenmark P, Ott M. Structural basis for the interaction of the chaperone Cbp3 with newly synthesized cytochrome during mitochondrial respiratory chain assembly. The Journal of Biological Chemistry. PMID 31537648 DOI: 10.1074/Jbc.Ra119.010483 |
0.343 |
|
| 2019 |
Basile W, Salvatore M, Bassot C, Elofsson A. Why do eukaryotic proteins contain more intrinsically disordered regions? Plos Computational Biology. 15: e1007186. PMID 31329574 DOI: 10.1371/Journal.Pcbi.1007186 |
0.438 |
|
| 2019 |
Cheng J, Choe MH, Elofsson A, Han KS, Hou J, Maghrabi AHA, McGuffin LJ, Menéndez-Hurtado D, Olechnovič K, Schwede T, Studer G, Uziela K, Venclovas Č, Wallner B. Estimation of model accuracy in CASP13. Proteins. PMID 31265154 DOI: 10.1002/Prot.25767 |
0.594 |
|
| 2019 |
Bassot C, Menendez Hurtado D, Elofsson A. Using PconsC4 and PconsFold2 to Predict Protein Structure. Current Protocols in Bioinformatics. e75. PMID 31063641 DOI: 10.1002/Cpbi.75 |
0.493 |
|
| 2019 |
Lamb J, Jarmolinska AI, Michel M, Menéndez-Hurtado D, Sulkowska JI, Elofsson A. PconsFam: An interactive database of structure predictions of Pfam families. Journal of Molecular Biology. PMID 30796988 DOI: 10.1016/J.Jmb.2019.01.047 |
0.398 |
|
| 2019 |
Hu H, Li Z, Elofsson A, Xie S. A Bi-LSTM Based Ensemble Algorithm for Prediction of Protein Secondary Structure Applied Sciences. 9: 3538. DOI: 10.3390/app9173538 |
0.345 |
|
| 2018 |
Michel M, Hurtado DM, Elofsson A. PconsC4: fast, accurate, and hassle-free contact predictions. Bioinformatics (Oxford, England). PMID 30590407 DOI: 10.1093/Bioinformatics/Bty1036 |
0.331 |
|
| 2018 |
Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A. Improved protein model quality assessments by changing the target function. Proteins. PMID 29524250 DOI: 10.1002/Prot.25492 |
0.617 |
|
| 2017 |
Tsirigos KD, Govindarajan S, Bassot C, Västermark Å, Lamb J, Shu N, Elofsson A. Topology of membrane proteins-predictions, limitations and variations. Current Opinion in Structural Biology. 50: 9-17. PMID 29100082 DOI: 10.1016/J.Sbi.2017.10.003 |
0.556 |
|
| 2017 |
Elofsson A, Joo K, Keasar C, Lee J, Maghrabi AHA, Manavalan B, McGuffin LJ, Ménendez Hurtado D, Mirabello C, Pilstål R, Sidi T, Uziela K, Wallner B. Methods for estimation of model accuracy in CASP12. Proteins. PMID 28975666 DOI: 10.1002/Prot.25395 |
0.574 |
|
| 2017 |
Salvatore M, Shu N, Elofsson A. The SubCons web-server: A user friendly web interface for state-of-the-art subcellular localization prediction. Protein Science : a Publication of the Protein Society. PMID 28901589 DOI: 10.1002/Pro.3297 |
0.434 |
|
| 2017 |
Michel M, Menéndez Hurtado D, Uziela K, Elofsson A. Large-scale structure prediction by improved contact predictions and model quality assessment. Bioinformatics (Oxford, England). 33: i23-i29. PMID 28881974 DOI: 10.1093/Bioinformatics/Btx239 |
0.417 |
|
| 2017 |
Michel M, Skwark MJ, Menéndez Hurtado D, Ekeberg M, Elofsson A. Predicting accurate contacts in thousands of Pfam domain families using PconsC3. Bioinformatics (Oxford, England). PMID 28535189 DOI: 10.1093/Bioinformatics/Btx332 |
0.774 |
|
| 2017 |
Salvatore M, Warholm P, Shu N, Basile W, Elofsson A. SubCons: a new ensemble method for improved human subcellular localization predictions. Bioinformatics (Oxford, England). PMID 28407043 DOI: 10.1093/Bioinformatics/Btx219 |
0.401 |
|
| 2017 |
Basile W, Sachenkova O, Light S, Elofsson A. High GC content causes orphan proteins to be intrinsically disordered. Plos Computational Biology. 13: e1005375. PMID 28355220 DOI: 10.1371/Journal.Pcbi.1005375 |
0.695 |
|
| 2017 |
Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A. ProQ3D: Improved model quality assessments using Deep Learning. Bioinformatics (Oxford, England). PMID 28052925 DOI: 10.1093/Bioinformatics/Btw819 |
0.553 |
|
| 2016 |
Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27965415 DOI: 10.1093/Nar/Gkw1279 |
0.378 |
|
| 2016 |
Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27899601 DOI: 10.1093/Nar/Gkw1056 |
0.402 |
|
| 2016 |
Uziela K, Shu N, Wallner B, Elofsson A. ProQ3: Improved model quality assessments using Rosetta energy terms. Scientific Reports. 6: 33509. PMID 27698390 DOI: 10.1038/Srep33509 |
0.6 |
|
| 2016 |
Tsirigos KD, Elofsson A, Bagos PG. PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. Bioinformatics (Oxford, England). 32: i665-i671. PMID 27587687 DOI: 10.1093/Bioinformatics/Btw444 |
0.466 |
|
| 2016 |
Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A. Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins. Bioinformatics (Oxford, England). PMID 26794316 DOI: 10.1093/Bioinformatics/Btw025 |
0.422 |
|
| 2015 |
Peters C, Tsirigos KD, Shu N, Elofsson A. Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics (Oxford, England). PMID 26644416 DOI: 10.1093/Bioinformatics/Btv709 |
0.523 |
|
| 2015 |
Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, et al. Molecular architecture of the active mitochondrial protein gate. Science (New York, N.Y.). 349: 1544-8. PMID 26404837 DOI: 10.1126/Science.Aac6428 |
0.36 |
|
| 2015 |
De Marothy MT, Elofsson A. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding. Protein Science : a Publication of the Protein Society. 24: 1057-74. PMID 25970811 DOI: 10.1002/Pro.2698 |
0.5 |
|
| 2015 |
Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Research. 43: W401-7. PMID 25969446 DOI: 10.7490/F1000Research.1110123.1 |
0.519 |
|
| 2015 |
Mirzadeh K, Martínez V, Toddo S, Guntur S, Herrgård MJ, Elofsson A, Nørholm MH, Daley DO. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction. Acs Synthetic Biology. PMID 25951437 DOI: 10.1021/Acssynbio.5B00033 |
0.337 |
|
| 2015 |
Hayat S, Sander C, Marks DS, Elofsson A. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences. Proceedings of the National Academy of Sciences of the United States of America. 112: 5413-8. PMID 25858953 DOI: 10.1073/Pnas.1419956112 |
0.477 |
|
| 2015 |
Uziela K, Shu N, Wallner B, Elofsson A. The newest developments of ProQ2 F1000research. 4. DOI: 10.7490/F1000Research.1110154.1 |
0.469 |
|
| 2014 |
Skwark MJ, Raimondi D, Michel M, Elofsson A. Improved contact predictions using the recognition of protein like contact patterns. Plos Computational Biology. 10: e1003889. PMID 25375897 DOI: 10.1371/Journal.Pcbi.1003889 |
0.798 |
|
| 2014 |
Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics (Oxford, England). 30: i482-8. PMID 25161237 DOI: 10.1093/Bioinformatics/Btu458 |
0.779 |
|
| 2014 |
Light S, Basile W, Elofsson A. Orphans and new gene origination, a structural and evolutionary perspective. Current Opinion in Structural Biology. 26: 73-83. PMID 24934869 DOI: 10.1016/J.Sbi.2014.05.006 |
0.666 |
|
| 2014 |
Virkki MT, Peters C, Nilsson D, Sörensen T, Cristobal S, Wallner B, Elofsson A. The positive inside rule is stronger when followed by a transmembrane helix. Journal of Molecular Biology. 426: 2982-91. PMID 24927974 DOI: 10.1016/J.Jmb.2014.06.002 |
0.617 |
|
| 2014 |
Virkki M, Boekel C, Illergård K, Peters C, Shu N, Tsirigos KD, Elofsson A, von Heijne G, Nilsson I. Large tilts in transmembrane helices can be induced during tertiary structure formation. Journal of Molecular Biology. 426: 2529-38. PMID 24793448 DOI: 10.1016/J.Jmb.2014.04.020 |
0.832 |
|
| 2014 |
Virkki MT, Agrawal N, Edsbäcker E, Cristobal S, Elofsson A, Kauko A. Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Science : a Publication of the Protein Society. 23: 981-92. PMID 24777974 DOI: 10.1002/Pro.2483 |
0.472 |
|
| 2014 |
Peters C, Elofsson A. Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins. 82: 2190-8. PMID 24753217 DOI: 10.1002/Prot.24582 |
0.335 |
|
| 2014 |
Uziela K, Shu N, Wallner B, Elofsson A. How to select the best protein model using ProQ2 F1000research. 5. DOI: 10.7490/F1000Research.1096842.1 |
0.601 |
|
| 2013 |
Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A. Protein expansion is primarily due to indels in intrinsically disordered regions. Molecular Biology and Evolution. 30: 2645-53. PMID 24037790 DOI: 10.1093/Molbev/Mst157 |
0.792 |
|
| 2013 |
Skwark MJ, Elofsson A. PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. Bioinformatics (Oxford, England). 29: 1817-8. PMID 23677942 DOI: 10.1093/Bioinformatics/Btt272 |
0.749 |
|
| 2013 |
Skwark MJ, Abdel-Rehim A, Elofsson A. PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics (Oxford, England). 29: 1815-6. PMID 23658418 DOI: 10.1093/Bioinformatics/Btt259 |
0.767 |
|
| 2013 |
Light S, Elofsson A. The impact of splicing on protein domain architecture. Current Opinion in Structural Biology. 23: 451-8. PMID 23562110 DOI: 10.1016/J.Sbi.2013.02.013 |
0.714 |
|
| 2013 |
Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A. Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics. 13: 1467-80. PMID 23512833 DOI: 10.1002/Pmic.201200517 |
0.78 |
|
| 2013 |
Light S, Sagit R, Ekman D, Elofsson A. Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins. Biochimica Et Biophysica Acta. 1834: 890-7. PMID 23333420 DOI: 10.1016/J.Bbapap.2013.01.002 |
0.8 |
|
| 2013 |
Bañó-Polo M, Martínez-Gil L, Wallner B, Nieva JL, Elofsson A, Mingarro I. Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. Journal of Molecular Biology. 425: 830-40. PMID 23228331 DOI: 10.1016/J.Jmb.2012.12.001 |
0.687 |
|
| 2013 |
Imai K, Hayat S, Sakiyama N, Fujita N, Tomii K, Elofsson A, Horton P. Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods in Molecular Biology (Clifton, N.J.). 939: 115-40. PMID 23192545 DOI: 10.1007/978-1-62703-107-3_10 |
0.544 |
|
| 2012 |
Hayat S, Elofsson A. Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions. Bioinformatics (Oxford, England). 28: i90-6. PMID 22689784 DOI: 10.1093/Bioinformatics/Bts233 |
0.405 |
|
| 2012 |
Tsirigos KD, Hennerdal A, Käll L, Elofsson A. A guideline to proteome-wide α-helical membrane protein topology predictions. Proteomics. 12: 2282-94. PMID 22685073 DOI: 10.1002/Pmic.201100495 |
0.848 |
|
| 2012 |
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071 |
0.503 |
|
| 2012 |
Light S, Sagit R, Ithychanda SS, Qin J, Elofsson A. The evolution of filamin-a protein domain repeat perspective. Journal of Structural Biology. 179: 289-98. PMID 22414427 DOI: 10.1016/J.Jsb.2012.02.010 |
0.795 |
|
| 2012 |
Hayat S, Elofsson A. BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. Bioinformatics (Oxford, England). 28: 516-22. PMID 22247276 DOI: 10.1093/Bioinformatics/Btr710 |
0.488 |
|
| 2012 |
Contreras FX, Ernst AM, Haberkant P, Björkholm P, Lindahl E, Gönen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brügger B. Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature. 481: 525-9. PMID 22230960 DOI: 10.1038/Nature10742 |
0.681 |
|
| 2012 |
Nørholm MH, Light S, Virkki MT, Elofsson A, von Heijne G, Daley DO. Manipulating the genetic code for membrane protein production: what have we learnt so far? Biochimica Et Biophysica Acta. 1818: 1091-6. PMID 21884679 DOI: 10.1016/J.Bbamem.2011.08.018 |
0.766 |
|
| 2012 |
Peters C, Hayat S, Elofsson A. A fast and accurate method for large-scale transmembrane beta barrel topology prediction F1000research. 3. DOI: 10.7490/F1000Research.1092192.1 |
0.423 |
|
| 2011 |
Hedin LE, Illergård K, Elofsson A. An introduction to membrane proteins. Journal of Proteome Research. 10: 3324-31. PMID 21815691 DOI: 10.1021/Pr200145A |
0.839 |
|
| 2011 |
Shu N, Elofsson A. KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics (Oxford, England). 27: 1702-3. PMID 21505030 DOI: 10.1093/Bioinformatics/Btr235 |
0.362 |
|
| 2011 |
Hennerdal A, Elofsson A. Rapid membrane protein topology prediction. Bioinformatics (Oxford, England). 27: 1322-3. PMID 21493661 DOI: 10.1093/Bioinformatics/Btr119 |
0.837 |
|
| 2011 |
Larsson P, Skwark MJ, Wallner B, Elofsson A. Improved predictions by Pcons.net using multiple templates. Bioinformatics (Oxford, England). 27: 426-7. PMID 21149277 DOI: 10.1093/Bioinformatics/Btq664 |
0.817 |
|
| 2011 |
Illergård K, Kauko A, Elofsson A. Why are polar residues within the membrane core evolutionary conserved? Proteins. 79: 79-91. PMID 20938980 DOI: 10.1002/Prot.22859 |
0.836 |
|
| 2010 |
Lima Mde F, Eloy NB, Pegoraro C, Sagit R, Rojas C, Bretz T, Vargas L, Elofsson A, de Oliveira AC, Hemerly AS, Ferreira PC. Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. Bmc Plant Biology. 10: 254. PMID 21087491 DOI: 10.1186/1471-2229-10-254 |
0.765 |
|
| 2010 |
Hennerdal A, Falk J, Lindahl E, Elofsson A. Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Science : a Publication of the Protein Society. 19: 2305-18. PMID 20882639 DOI: 10.1002/Pro.510 |
0.839 |
|
| 2010 |
Björklund AK, Light S, Sagit R, Elofsson A. Nebulin: a study of protein repeat evolution. Journal of Molecular Biology. 402: 38-51. PMID 20643138 DOI: 10.1016/J.Jmb.2010.07.011 |
0.809 |
|
| 2010 |
Illergård K, Callegari S, Elofsson A. MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane. Bmc Bioinformatics. 11: 333. PMID 20565847 DOI: 10.1186/1471-2105-11-333 |
0.853 |
|
| 2010 |
Kauko A, Hedin LE, Thebaud E, Cristobal S, Elofsson A, von Heijne G. Repositioning of transmembrane alpha-helices during membrane protein folding. Journal of Molecular Biology. 397: 190-201. PMID 20109468 DOI: 10.1016/J.Jmb.2010.01.042 |
0.768 |
|
| 2010 |
Ekman D, Elofsson A. Identifying and quantifying orphan protein sequences in fungi. Journal of Molecular Biology. 396: 396-405. PMID 19944701 DOI: 10.1016/J.Jmb.2009.11.053 |
0.7 |
|
| 2010 |
Hedin LE, Ojemalm K, Bernsel A, Hennerdal A, Illergård K, Enquist K, Kauko A, Cristobal S, von Heijne G, Lerch-Bader M, Nilsson I, Elofsson A. Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. Journal of Molecular Biology. 396: 221-9. PMID 19931281 DOI: 10.1016/J.Jmb.2009.11.036 |
0.81 |
|
| 2009 |
Larsson P, Skwark MJ, Wallner B, Elofsson A. Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins. 77: 167-72. PMID 19544566 DOI: 10.1002/Prot.22476 |
0.79 |
|
| 2009 |
Illergård K, Ardell DH, Elofsson A. Structure is three to ten times more conserved than sequence--a study of structural response in protein cores. Proteins. 77: 499-508. PMID 19507241 DOI: 10.1002/Prot.22458 |
0.808 |
|
| 2009 |
Bernsel A, Viklund H, Hennerdal A, Elofsson A. TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Research. 37: W465-8. PMID 19429891 DOI: 10.1093/Nar/Gkp363 |
0.814 |
|
| 2008 |
Viklund H, Bernsel A, Skwark M, Elofsson A. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics (Oxford, England). 24: 2928-9. PMID 18945683 DOI: 10.1093/Bioinformatics/Btn550 |
0.796 |
|
| 2008 |
Björklund AK, Light S, Hedin L, Elofsson A. Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics. 8: 4657-67. PMID 18924110 DOI: 10.1002/Pmic.200800150 |
0.824 |
|
| 2008 |
Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. Arrangements in the modular evolution of proteins. Trends in Biochemical Sciences. 33: 444-51. PMID 18656364 DOI: 10.1016/J.Tibs.2008.05.008 |
0.812 |
|
| 2008 |
Kauko A, Illergård K, Elofsson A. Coils in the membrane core are conserved and functionally important. Journal of Molecular Biology. 380: 170-80. PMID 18511074 DOI: 10.1016/J.Jmb.2008.04.052 |
0.83 |
|
| 2008 |
Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A. Prediction of membrane-protein topology from first principles. Proceedings of the National Academy of Sciences of the United States of America. 105: 7177-81. PMID 18477697 DOI: 10.1073/Pnas.0711151105 |
0.842 |
|
| 2008 |
Viklund H, Elofsson A. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics (Oxford, England). 24: 1662-8. PMID 18474507 DOI: 10.1093/Bioinformatics/Btn221 |
0.855 |
|
| 2008 |
Larsson P, Wallner B, Lindahl E, Elofsson A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein Science : a Publication of the Protein Society. 17: 990-1002. PMID 18441233 DOI: 10.1110/Ps.073344908 |
0.642 |
|
| 2008 |
Papaloukas C, Granseth E, Viklund H, Elofsson A. Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Science : a Publication of the Protein Society. 17: 271-8. PMID 18096645 DOI: 10.1110/Ps.073036108 |
0.826 |
|
| 2008 |
Bernsel A, Viklund H, Elofsson A. Remote homology detection of integral membrane proteins using conserved sequence features. Proteins. 71: 1387-99. PMID 18076048 DOI: 10.1002/Prot.21825 |
0.848 |
|
| 2008 |
Wallner B, Elofsson A. Quality Assessment of Protein Models Prediction of Protein Structures, Functions, and Interactions. 143-157. DOI: 10.1002/9780470741894.ch6 |
0.529 |
|
| 2007 |
Wallner B, Elofsson A. Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins. 69: 184-93. PMID 17894353 DOI: 10.1002/Prot.21774 |
0.607 |
|
| 2007 |
Ekman D, Björklund AK, Elofsson A. Quantification of the elevated rate of domain rearrangements in metazoa. Journal of Molecular Biology. 372: 1337-48. PMID 17689563 DOI: 10.1016/J.Jmb.2007.06.022 |
0.782 |
|
| 2007 |
Wallner B, Larsson P, Elofsson A. Pcons.net: protein structure prediction meta server. Nucleic Acids Research. 35: W369-74. PMID 17584798 DOI: 10.1093/Nar/Gkm319 |
0.737 |
|
| 2007 |
Elofsson A, von Heijne G. Membrane protein structure: prediction versus reality. Annual Review of Biochemistry. 76: 125-40. PMID 17579561 DOI: 10.1146/Annurev.Biochem.76.052705.163539 |
0.661 |
|
| 2007 |
Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA. Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biology. 8: 213. PMID 17521457 DOI: 10.1186/Gb-2007-8-5-213 |
0.593 |
|
| 2006 |
Björklund AK, Ekman D, Elofsson A. Expansion of protein domain repeats. Plos Computational Biology. 2: e114. PMID 16933986 DOI: 10.1371/Journal.Pcbi.0020114 |
0.796 |
|
| 2006 |
Granseth E, Viklund H, Elofsson A. ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Bioinformatics (Oxford, England). 22: e191-6. PMID 16873471 DOI: 10.1093/Bioinformatics/Btl206 |
0.836 |
|
| 2006 |
Ohlson T, Aggarwal V, Elofsson A, MacCallum RM. Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. Bmc Bioinformatics. 7: 357. PMID 16869963 DOI: 10.1186/1471-2105-7-357 |
0.434 |
|
| 2006 |
Viklund H, Granseth E, Elofsson A. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. Journal of Molecular Biology. 361: 591-603. PMID 16860824 DOI: 10.1016/J.Jmb.2006.06.037 |
0.822 |
|
| 2006 |
Amico M, Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D, Krogh A, Fariselli P, Luigi Martelli P, Casadio R. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Research. 34: W169-72. PMID 16844984 DOI: 10.1093/Nar/Gkl208 |
0.827 |
|
| 2006 |
Ekman D, Light S, Björklund AK, Elofsson A. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biology. 7: R45. PMID 16780599 DOI: 10.1186/Gb-2006-7-6-R45 |
0.829 |
|
| 2006 |
Wallner B, Elofsson A. Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Science : a Publication of the Protein Society. 15: 900-13. PMID 16522791 DOI: 10.1110/Ps.051799606 |
0.611 |
|
| 2006 |
Björklund A, Thorén A, von Heijne G, Elofsson A. The use of phylogenetic profiles for gene predictions revisited Current Genomics. 7: 79-86. DOI: 10.2174/138920206777304650 |
0.711 |
|
| 2005 |
Light S, Kraulis P, Elofsson A. Preferential attachment in the evolution of metabolic networks. Bmc Genomics. 6: 159. PMID 16281983 DOI: 10.1186/1471-2164-6-159 |
0.575 |
|
| 2005 |
Ohlson T, Elofsson A. ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. Bmc Bioinformatics. 6: 253. PMID 16225676 DOI: 10.1186/1471-2105-6-253 |
0.402 |
|
| 2005 |
Wallner B, Elofsson A. Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics (Oxford, England). 21: 4248-54. PMID 16204344 DOI: 10.1093/Bioinformatics/Bti702 |
0.607 |
|
| 2005 |
Björklund AK, Ekman D, Light S, Frey-Skött J, Elofsson A. Domain rearrangements in protein evolution. Journal of Molecular Biology. 353: 911-23. PMID 16198373 DOI: 10.1016/J.Jmb.2005.08.067 |
0.813 |
|
| 2005 |
Berglund AC, Wallner B, Elofsson A, Liberles DA. Tertiary windowing to detect positive diversifying selection. Journal of Molecular Evolution. 60: 499-504. PMID 15883884 DOI: 10.1007/S00239-004-0223-4 |
0.564 |
|
| 2005 |
Wallner B, Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Science : a Publication of the Protein Society. 14: 1315-27. PMID 15840834 DOI: 10.1110/Ps.041253405 |
0.553 |
|
| 2005 |
Ekman D, Björklund AK, Frey-Skött J, Elofsson A. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. Journal of Molecular Biology. 348: 231-43. PMID 15808866 DOI: 10.1016/J.Jmb.2005.02.007 |
0.787 |
|
| 2005 |
Granseth E, von Heijne G, Elofsson A. A study of the membrane-water interface region of membrane proteins. Journal of Molecular Biology. 346: 377-85. PMID 15663952 DOI: 10.1016/J.Jmb.2004.11.036 |
0.834 |
|
| 2004 |
Ohlson T, Wallner B, Elofsson A. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins. 57: 188-97. PMID 15326603 DOI: 10.1002/Prot.20184 |
0.61 |
|
| 2004 |
Viklund H, Elofsson A. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Science : a Publication of the Protein Society. 13: 1908-17. PMID 15215532 DOI: 10.1110/Ps.04625404 |
0.849 |
|
| 2004 |
Wallner B, Fang H, Ohlson T, Frey-Skött J, Elofsson A. Using evolutionary information for the query and target improves fold recognition. Proteins. 54: 342-50. PMID 14696196 DOI: 10.1002/Prot.10565 |
0.598 |
|
| 2003 |
Rychlewski L, Fischer D, Elofsson A. LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins. 53: 542-7. PMID 14579344 DOI: 10.1002/Prot.10535 |
0.361 |
|
| 2003 |
Wallner B, Fang H, Elofsson A. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins. 53: 534-41. PMID 14579343 DOI: 10.1002/Prot.10536 |
0.623 |
|
| 2003 |
Emanuelsson O, Elofsson A, von Heijne G, Cristóbal S. In silico prediction of the peroxisomal proteome in fungi, plants and animals. Journal of Molecular Biology. 330: 443-56. PMID 12823981 DOI: 10.1016/S0022-2836(03)00553-9 |
0.628 |
|
| 2003 |
Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (Oxford, England). 19: 1015-8. PMID 12761065 DOI: 10.1093/Bioinformatics/Btg124 |
0.441 |
|
| 2003 |
Wallner B, Elofsson A. Can correct protein models be identified? Protein Science : a Publication of the Protein Society. 12: 1073-86. PMID 12717029 DOI: 10.1110/Ps.0236803 |
0.642 |
|
| 2002 |
Hedman M, Deloof H, Von Heijne G, Elofsson A. Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Science : a Publication of the Protein Society. 11: 652-8. PMID 11847287 DOI: 10.1110/Ps.39402 |
0.692 |
|
| 2002 |
Elofsson A. A study on protein sequence alignment quality. Proteins. 46: 330-9. PMID 11835508 DOI: 10.1002/Prot.10043 |
0.392 |
|
| 2002 |
Liberles DA, Thorén A, von Heijne G, Elofsson A. The use of phylogenetic profiles for gene predictions Current Genomics. 3: 131-137. DOI: 10.2174/1389202023350499 |
0.529 |
|
| 2001 |
Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins. 184-91. PMID 11835496 DOI: 10.1002/Prot.10039 |
0.403 |
|
| 2001 |
Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack RL. CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins. 171-83. PMID 11835495 DOI: 10.1002/Prot.10036 |
0.362 |
|
| 2001 |
Lundström J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Science : a Publication of the Protein Society. 10: 2354-62. PMID 11604541 DOI: 10.1110/Ps.08501 |
0.465 |
|
| 2001 |
Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. A study of quality measures for protein threading models. Bmc Bioinformatics. 2: 5. PMID 11545673 DOI: 10.1186/1471-2105-2-5 |
0.369 |
|
| 2001 |
Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. Structure prediction meta server. Bioinformatics (Oxford, England). 17: 750-1. PMID 11524381 DOI: 10.1093/Bioinformatics/17.8.750 |
0.362 |
|
| 2001 |
Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Science : a Publication of the Protein Society. 10: 352-61. PMID 11266621 DOI: 10.1110/Ps.40501 |
0.424 |
|
| 2000 |
Fischer D, Elofsson A, Rychlewski L. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2. Protein Engineering. 13: 667-70. PMID 11112504 DOI: 10.1093/Protein/13.10.667 |
0.411 |
|
| 2000 |
Lindahl E, Elofsson A. Identification of related proteins on family, superfamily and fold level. Journal of Molecular Biology. 295: 613-25. PMID 10623551 DOI: 10.1006/Jmbi.1999.3377 |
0.47 |
|
| 1999 |
Monné M, Nilsson I, Elofsson A, von Heijne G. Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale. Journal of Molecular Biology. 293: 807-14. PMID 10543969 DOI: 10.1006/Jmbi.1999.3183 |
0.573 |
|
| 1999 |
Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins. 209-17. PMID 10526371 DOI: 10.1002/(Sici)1097-0134(1999)37:3+<209::Aid-Prot27>3.0.Co;2-Y |
0.408 |
|
| 1999 |
Elofsson A, Sonnhammer EL. A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics (Oxford, England). 15: 480-500. PMID 10383473 DOI: 10.1093/Bioinformatics/15.6.480 |
0.42 |
|
| 1999 |
Hargbo J, Elofsson A. Hidden Markov models that use predicted secondary structures for fold recognition. Proteins. 36: 68-76. PMID 10373007 DOI: 10.1002/(Sici)1097-0134(19990701)36:1<68::Aid-Prot6>3.0.Co;2-1 |
0.51 |
|
| 1999 |
Zhang XP, Elofsson A, Andreu D, Glaser E. Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70. Journal of Molecular Biology. 288: 177-90. PMID 10329135 DOI: 10.1006/Jmbi.1999.2669 |
0.314 |
|
| 1998 |
Seshadri K, Garemyr R, Wallin E, von Heijne G, Elofsson A. Architecture of beta-barrel membrane proteins: analysis of trimeric porins. Protein Science : a Publication of the Protein Society. 7: 2026-32. PMID 9761484 DOI: 10.1002/Pro.5560070919 |
0.632 |
|
| 1997 |
Mingarro I, Elofsson A, von Heijne G. Helix-helix packing in a membrane-like environment. Journal of Molecular Biology. 272: 633-41. PMID 9325117 DOI: 10.1006/Jmbi.1997.1276 |
0.603 |
|
| 1997 |
Cserzö M, Wallin E, Simon I, von Heijne G, Elofsson A. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Engineering. 10: 673-6. PMID 9278280 DOI: 10.1093/Protein/10.6.673 |
0.682 |
|
| 1997 |
Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Science : a Publication of the Protein Society. 6: 808-15. PMID 9098890 DOI: 10.1002/Pro.5560060407 |
0.633 |
|
| 1996 |
Fischer D, Elofsson A, Rice D, Eisenberg D. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 300-18. PMID 9390240 |
0.5 |
|
| 1996 |
Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D. A study of combined structure/sequence profiles. Folding & Design. 1: 451-61. PMID 9080191 DOI: 10.1016/S1359-0278(96)00061-2 |
0.545 |
|
| 1996 |
Elofsson A, Nilsson L. A 1.2 ns molecular dynamics simulation of the ribonuclease T1-3′-guanosine monophosphate complex Journal of Physical Chemistry. 100: 2480-2488. DOI: 10.1021/Jp952517G |
0.462 |
|
| 1995 |
Elofsson A, Le Grand SM, Eisenberg D. Local moves: an efficient algorithm for simulation of protein folding. Proteins. 23: 73-82. PMID 8539252 DOI: 10.1002/Prot.340230109 |
0.445 |
|
| 1993 |
Elofsson A, Nilsson L. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. Journal of Molecular Biology. 233: 766-80. PMID 8411178 DOI: 10.1006/Jmbi.1993.1551 |
0.447 |
|
| 1993 |
Elofsson A, Kulinski T, Rigler R, Nilsson L. Site specific point mutation changes specificity: a molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions. Proteins. 17: 161-75. PMID 8265564 DOI: 10.1002/Prot.340170206 |
0.605 |
|
| 1993 |
Elofsson A, Nilsson L. Free Energy Perturbations in Ribonuclease T1Substrate Binding. A Study of the Influence of Simulation Length, Internal Degrees of Freedom and Structure in Free Energy Perturbations Molecular Simulation. 10: 255-276. DOI: 10.1080/08927029308022168 |
0.439 |
|
| 1992 |
Wennerberg A, De Loof H, Kulinski T, Elofsson A, Nilsson L, Rigler R. Study of the distribution function of the three-dimensional structures of rat galanin determined by two-dimensional 1H NMR, distance geometry calculations, molecular dynamics and energy transfer measurements Regulatory Peptides. 37: S175. DOI: 10.1016/0167-0115(92)91030-4 |
0.578 |
|
| 1991 |
Elofsson A, Rigler R, Nilsson L, Roslund J, Krause G, Holmgren A. Motion of aromatic side chains, picosecond fluorescence, and internal energy transfer in Escherichia coli thioredoxin studied by site-directed mutagenesis, time-resolved fluorescence spectroscopy, and molecular dynamics simulations. Biochemistry. 30: 9648-56. PMID 1911751 DOI: 10.1021/Bi00104A012 |
0.593 |
|
| 1990 |
Elofsson A, Nilsson L, Rigler R. Studies on somatostatin with time-resolved spectroscopy and molecular dynamics simulations. International Journal of Peptide and Protein Research. 36: 297-301. PMID 1980672 DOI: 10.1111/J.1399-3011.1990.Tb00982.X |
0.592 |
|
| 1988 |
Elofsson A, Ghosh I, MacKerell A, Nilsson L, Rigler R. Molecular structure, dynamics and function of signal and transmitter peptides Regulatory Peptides. 22: 63. DOI: 10.1016/0167-0115(88)90283-2 |
0.591 |
|
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