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Björn Wallner, Ph.D - Publications

Affiliations: 
IFM Linköping University, Linköping, Östergötlands län, Sweden 
Area:
Protein bioinformatics
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48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, ... ... Wallner B, et al. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins. PMID 37905971 DOI: 10.1002/prot.26609  0.392
2023 Wallner B. AFsample: improving multimer prediction with AlphaFold using massive sampling. Bioinformatics (Oxford, England). 39. PMID 37713472 DOI: 10.1093/bioinformatics/btad573  0.337
2023 Wallner B. Improved multimer prediction using massive sampling with AlphaFold in CASP15. Proteins. PMID 37548092 DOI: 10.1002/prot.26562  0.328
2022 Johansson-Åkhe I, Wallner B. Improving peptide-protein docking with AlphaFold-Multimer using forced sampling. Frontiers in Bioinformatics. 2: 959160. PMID 36304330 DOI: 10.3389/fbinf.2022.959160  0.339
2022 Johansson-Åkhe I, Wallner B. InterPepScore: A Deep Learning Score for Improving the FlexPepDock Refinement Protocol. Bioinformatics (Oxford, England). PMID 35575349 DOI: 10.1093/bioinformatics/btac325  0.344
2020 Mirabello C, Wallner B. InterLig: Improved ligand-based virtual screening using topologically-independent structural alignments. Bioinformatics (Oxford, England). PMID 32049311 DOI: 10.1093/Bioinformatics/Btaa089  0.334
2020 Johansson-Åkhe I, Mirabello C, Wallner B. InterPep2: Global Peptide-Protein Docking using Interaction Surface Templates. Bioinformatics (Oxford, England). PMID 31917413 DOI: 10.1093/Bioinformatics/Btaa005  0.306
2019 Mirabello C, Wallner B. rawMSA: End-to-end Deep Learning using raw Multiple Sequence Alignments. Plos One. 14: e0220182. PMID 31415569 DOI: 10.1371/Journal.Pone.0220182  0.434
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  0.668
2019 Johansson-Åkhe I, Mirabello C, Wallner B. Predicting protein-peptide interaction sites using distant protein complexes as structural templates. Scientific Reports. 9: 4267. PMID 30862810 DOI: 10.1038/S41598-019-38498-7  0.354
2018 Mirabello C, Wallner B. Topology independent structural matching discovers novel templates for protein interfaces. Bioinformatics (Oxford, England). 34: i787-i794. PMID 30423106 DOI: 10.1093/Bioinformatics/Bty587  0.384
2018 Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8  0.301
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  0.687
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  0.666
2017 Wallenhammar A, Anandapadamanaban M, Lemak A, Mirabello C, Lundström P, Wallner B, Sunnerhagen M. Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain. Plos One. 12: e0181551. PMID 28753623 DOI: 10.1371/Journal.Pone.0181551  0.305
2017 Basu S, Söderquist F, Wallner B. Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins. Journal of Computer-Aided Molecular Design. PMID 28365882 DOI: 10.1007/S10822-017-0020-Y  0.395
2017 Mirabello C, Wallner B. InterPred: A pipeline to identify and model protein-protein interactions. Proteins. PMID 28263438 DOI: 10.1002/Prot.25280  0.466
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  0.597
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  0.68
2016 Basu S, Wallner B. DockQ: A Quality Measure for Protein-Protein Docking Models. Plos One. 11: e0161879. PMID 27560519 DOI: 10.1371/Journal.Pone.0161879  0.524
2016 Basu S, Wallner B. Finding correct protein-protein docking models using ProQDock. Bioinformatics (Oxford, England). 32: i262-i270. PMID 27307625 DOI: 10.1093/Bioinformatics/Btw257  0.448
2016 Uziela K, Wallner B. ProQ2: Estimation of Model Accuracy Implemented in Rosetta. Bioinformatics (Oxford, England). PMID 26733453 DOI: 10.1093/Bioinformatics/Btv767  0.561
2015 Bunkóczi G, Wallner B, Read RJ. Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement. Structure (London, England : 1993). 23: 397-406. PMID 25619999 DOI: 10.1016/J.Str.2014.11.020  0.363
2015 Tu WB, Helander S, Pilstål R, Hickman KA, Lourenco C, Jurisica I, Raught B, Wallner B, Sunnerhagen M, Penn LZ. Myc and its interactors take shape. Biochimica Et Biophysica Acta. 1849: 469-483. PMID 24933113 DOI: 10.1016/J.Bbagrm.2014.06.002  0.337
2015 Uziela K, Shu N, Wallner B, Elofsson A. The newest developments of ProQ2 F1000research. 4. DOI: 10.7490/F1000Research.1110154.1  0.483
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  0.557
2014 Wallner B. ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling. Bioinformatics (Oxford, England). 30: 2221-3. PMID 24713439 DOI: 10.1093/Bioinformatics/Btu187  0.549
2014 Zamora-Ros R, Luján-Barroso L, Bueno-de-Mesquita HB, Dik VK, Boeing H, Steffen A, Tjønneland A, Olsen A, Bech BH, Overvad K, Boutron-Ruault MC, Racine A, Fagherazzi G, Kuhn T, Katzke V, ... ... Wallner B, et al. Tea and coffee consumption and risk of esophageal cancer: the European prospective investigation into cancer and nutrition study. International Journal of Cancer. Journal International Du Cancer. 135: 1470-9. PMID 24535727 DOI: 10.1002/ijc.28789  0.32
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  0.626
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  0.568
2012 Ray A, Lindahl E, Wallner B. Improved model quality assessment using ProQ2. Bmc Bioinformatics. 13: 224. PMID 22963006 DOI: 10.1186/1471-2105-13-224  0.567
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  0.777
2010 Bertaccini EJ, Wallner B, Trudell JR, Lindahl E. Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM4. Journal of Chemical Information and Modeling. 50: 2248-55. PMID 21117677 DOI: 10.1021/Ci100266C  0.365
2010 Ray A, Lindahl E, Wallner B. Model quality assessment for membrane proteins. Bioinformatics (Oxford, England). 26: 3067-74. PMID 20947525 DOI: 10.1093/Bioinformatics/Btq581  0.529
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  0.77
2009 Barth P, Wallner B, Baker D. Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences of the United States of America. 106: 1409-14. PMID 19190187 DOI: 10.1073/Pnas.0808323106  0.463
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  0.728
2008 Wallner B, Elofsson A. Quality Assessment of Protein Models Prediction of Protein Structures, Functions, and Interactions. 143-157. DOI: 10.1002/9780470741894.ch6  0.61
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  0.701
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  0.72
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  0.7
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  0.634
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  0.552
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  0.631
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  0.63
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  0.592
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  0.649
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  0.697
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