| 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 |
0.334 |
|
| 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 |
0.314 |
|
| 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 |
0.331 |
|
| 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 |
0.329 |
|
| 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 |
0.318 |
|
| 2019 |
Wei Y, Resetca D, Li Z, Johansson-Åkhe I, Ahlner A, Helander S, Wallenhammar A, Morad V, Raught B, Wallner B, Kokubo T, Tong Y, Penn LZ, Sunnerhagen M. Multiple direct interactions of TBP with the MYC oncoprotein. Nature Structural & Molecular Biology. PMID 31686052 DOI: 10.1038/S41594-019-0321-Z |
0.403 |
|
| 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 |
0.409 |
|
| 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 |
0.429 |
|
| 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 |
0.372 |
|
| 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 |
0.407 |
|
| 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 |
0.666 |
|
| 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 |
0.439 |
|
| 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 |
0.402 |
|
| 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 |
0.325 |
|
| 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 |
0.401 |
|
| 2017 |
Mirabello C, Wallner B. InterPred: A pipeline to identify and model protein-protein interactions. Proteins. PMID 28263438 DOI: 10.1002/Prot.25280 |
0.453 |
|
| 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 |
0.324 |
|
| 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 |
0.439 |
|
| 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 |
0.417 |
|
| 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 |
0.444 |
|
| 2016 |
Uziela K, Wallner B. ProQ2: Estimation of Model Accuracy Implemented in Rosetta. Bioinformatics (Oxford, England). PMID 26733453 DOI: 10.1093/Bioinformatics/Btv767 |
0.461 |
|
| 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 |
0.314 |
|
| 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 |
0.381 |
|
| 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 |
0.328 |
|
| 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 |
0.442 |
|
| 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 |
0.371 |
|
| 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 |
0.367 |
|
| 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 |
0.452 |
|
| 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 |
0.459 |
|
| 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 |
0.364 |
|
| 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 |
0.459 |
|
| 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 |
0.406 |
|
| 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 |
0.639 |
|
| 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 |
0.39 |
|
| 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 |
0.452 |
|
| 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 |
0.458 |
|
| 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 |
0.454 |
|
| 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 |
0.418 |
|
| 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 |
0.366 |
|
| 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 |
0.383 |
|
| 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 |
0.325 |
|
| 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 |
0.424 |
|
| 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 |
0.477 |
|
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