Alexandre MJJ Bonvin, Ph.D. - Publications

1989-1994 Chemistry Utrecht University, Utrecht, Netherlands 
 1994-1996 Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
 1996-1998 Physical Chemistry Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
 1998- Chemistry Utrecht University, Utrecht, Netherlands 
Protein-protein interactions, docking

147 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
2020 Basciu A, Malloci G, Koukos P, Pietrucci F, Bonvin AM, Vargiu AV. EDES: A Protocol to Generate Holo-Like and Druggable Protein Conformations Starting from the APO Structure Biophysical Journal. 118: 44a. DOI: 10.1016/j.bpj.2019.11.420  0.611
2017 Geng C, Narasimhan S, Rodrigues JP, Bonvin AM. Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. Methods in Molecular Biology (Clifton, N.J.). 1561: 109-138. PMID 28236236 DOI: 10.1007/978-1-4939-6798-8_8  0.805
2016 van Zundert GC, Trellet M, Schaarschmidt J, Kurkcuoglu Z, David M, Verlato M, Rosato A, Bonvin AM. The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes. Journal of Molecular Biology. PMID 27939290 DOI: 10.1016/J.Jmb.2016.11.032  0.793
2016 de Bruin RC, Stam AG, Vangone A, van Bergen En Henegouwen PM, Verheul HM, Sebestyén Z, Kuball J, Bonvin AM, de Gruijl TD, van der Vliet HJ. Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology (Baltimore, Md. : 1950). PMID 27895170 DOI: 10.4049/jimmunol.1600948  0.646
2016 Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI Round1. Proteins. PMID 27802573 DOI: 10.1002/Prot.25198  0.776
2016 Spiliotopoulos D, Kastritis PL, Melquiond AS, Bonvin AM, Musco G, Rocchia W, Spitaleri A. dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. Frontiers in Molecular Biosciences. 3: 46. PMID 27630991 DOI: 10.3389/Fmolb.2016.00046  0.813
2016 Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford, England). PMID 27503228 DOI: 10.1093/Bioinformatics/Btw514  0.83
2016 Melo R, Fieldhouse R, Melo A, Correia JD, Cordeiro MN, Gümüş ZH, Costa J, Bonvin AM, Moreira IS. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. International Journal of Molecular Sciences. 17. PMID 27472327 DOI: 10.3390/Ijms17081215  0.649
2016 Geng C, Vangone A, Bonvin AM. Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes. Protein Engineering, Design & Selection : Peds. PMID 27284087 DOI: 10.1093/protein/gzw020  0.8
2016 Liu Y, Rodrigues JP, Bonvin AM, Zaal EA, Berkers CR, Heger M, Gawarecka K, Swiezewska E, Breukink E, Egmond MR. New insight in the catalytic mechanism of bacterial MraY from enzyme kinetics and docking studies. The Journal of Biological Chemistry. PMID 27226570 DOI: 10.1074/jbc.M116.717884  0.498
2016 Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins. PMID 27172383 DOI: 10.1002/Prot.25063  0.39
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Bonvin AM, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.809
2016 Xue LC, Rodrigues JP, Dobbs D, Honavar V, Bonvin AM. Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings in Bioinformatics. PMID 27013645 DOI: 10.1093/bib/bbw027  0.651
2016 Jung S, Fischer J, Spudy B, Kerkow T, Sönnichsen FD, Xue L, Bonvin AM, Goettig P, Magdolen V, Meyer-Hoffert U, Grötzinger J. The solution structure of the kallikrein-related peptidases inhibitor SPINK6. Biochemical and Biophysical Research Communications. PMID 26828269 DOI: 10.1016/J.Bbrc.2016.01.172  0.454
2016 Rodrigues JP, Melquiond AS, Bonvin AM. Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. PMID 26751257 DOI: 10.1002/bmb.20941  0.787
2016 Trellet M, Schaarschmidt J, Zundert G, Kurkcuoglu Z, Melquiond A, Bonvin A. Integrative modelling goes HPC/HTC F1000research. 5. DOI: 10.7490/F1000Research.1113051.1  0.745
2015 Xue LC, Dobbs D, Bonvin AM, Honavar V. Computational prediction of protein interfaces: A review of data driven methods. Febs Letters. PMID 26460190 DOI: 10.1016/j.febslet.2015.10.003  0.555
2015 van Zundert GC, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, van Dijk M, de Vries SJ, Bonvin AM. The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology. PMID 26410586 DOI: 10.1016/J.Jmb.2015.09.014  0.783
2015 Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology. 427: 3031-41. PMID 26231283 DOI: 10.1016/J.Jmb.2015.07.016  0.824
2015 Vangone A, Bonvin AM. Contacts-based prediction of binding affinity in protein-protein complexes. Elife. 4: e07454. PMID 26193119 DOI: 10.7554/eLife.07454  0.83
2015 Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (London, England : 1993). PMID 26095030 DOI: 10.1016/J.Str.2015.05.013  0.546
2015 Sinnige T, Weingarth M, Daniëls M, Boelens R, Bonvin AM, Houben K, Baldus M. Conformational Plasticity of the POTRA 5 Domain in the Outer Membrane Protein Assembly Factor BamA. Structure (London, England : 1993). PMID 26027731 DOI: 10.1016/J.Str.2015.04.014  0.622
2015 Rad-Malekshahi M, Visscher KM, Rodrigues JP, de Vries R, Hennink WE, Baldus M, Bonvin AM, Mastrobattista E, Weingarth M. The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail. Journal of the American Chemical Society. 137: 7775-84. PMID 26022089 DOI: 10.1021/Jacs.5B02919  0.481
2015 van Zundert GC, Melquiond AS, Bonvin AM. Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data. Structure (London, England : 1993). 23: 949-60. PMID 25914056 DOI: 10.1016/j.str.2015.03.014  0.807
2015 Trellet M, Melquiond AS, Bonvin AM. Information-driven modeling of protein-peptide complexes. Methods in Molecular Biology (Clifton, N.J.). 1268: 221-39. PMID 25555727 DOI: 10.1007/978-1-4939-2285-7_10  0.805
2015 Visscher KM, Kastritis PL, Bonvin AM. Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins. 83: 445-58. PMID 25524313 DOI: 10.1002/Prot.24741  0.666
2015 Rodrigues JP, Karaca E, Bonvin AM. Information-driven structural modelling of protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 1215: 399-424. PMID 25330973 DOI: 10.1007/978-1-4939-1465-4_18  0.796
2015 Vranken WF, Vuister GW, Bonvin AM. NMR-based modeling and refinement of protein 3D structures. Methods in Molecular Biology (Clifton, N.J.). 1215: 351-80. PMID 25330971 DOI: 10.1007/978-1-4939-1465-4_16  0.61
2015 Vangone A, Bonvin AM. Author response: Contacts-based prediction of binding affinity in protein–protein complexes Elife. DOI: 10.7554/Elife.07454.018  0.713
2014 Ferguson FM, Dias DM, Rodrigues JP, Wienk H, Boelens R, Bonvin AM, Abell C, Ciulli A. Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking. Biochemistry. 53: 6706-16. PMID 25266743 DOI: 10.1021/Bi500909D  0.729
2014 Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS. Sequence co-evolution gives 3D contacts and structures of protein complexes. Elife. 3. PMID 25255213 DOI: 10.7554/Elife.03430  0.6
2014 Kastritis PL, Rodrigues JP, Folkers GE, Boelens R, Bonvin AM. Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface. Journal of Molecular Biology. 426: 2632-52. PMID 24768922 DOI: 10.1016/J.Jmb.2014.04.017  0.809
2014 Rodrigues JP, Bonvin AM. Integrative computational modeling of protein interactions. The Febs Journal. 281: 1988-2003. PMID 24588898 DOI: 10.1111/febs.12771  0.595
2014 van Zundert GC, Bonvin AM. Modeling protein-protein complexes using the HADDOCK webserver "modeling protein complexes with HADDOCK". Methods in Molecular Biology (Clifton, N.J.). 1137: 163-79. PMID 24573481 DOI: 10.1007/978-1-4939-0366-5_12  0.348
2014 Kastritis PL, Rodrigues JP, Bonvin AM. HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. Journal of Chemical Information and Modeling. 54: 826-36. PMID 24521147 DOI: 10.1021/Ci4005332  0.739
2014 Snijder J, Burnley RJ, Wiegard A, Melquiond AS, Bonvin AM, Axmann IM, Heck AJ. Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proceedings of the National Academy of Sciences of the United States of America. 111: 1379-84. PMID 24474762 DOI: 10.1073/Pnas.1314326111  0.806
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.795
2014 van der Cruijsen E, Visscher K, Rodrigues J, Bonvin A, Baldus M, Weingarth M. Ion Channel - Ion Channel Interaction at Atomic Resolution Biophysical Journal. 106: 628a. DOI: 10.1016/J.Bpj.2013.11.3474  0.521
2013 Bonvin A. Coming to peace with protein complexes? 5th CAPRI evaluation meeting, April 17-19th 2013 - Utrecht Proteins: Structure, Function and Bioinformatics. 81: 2073-2074. PMID 24277264 DOI: 10.1002/Prot.24431  0.47
2013 Janin J, Bonvin AM. Protein-protein interactions. Current Opinion in Structural Biology. 23: 859-61. PMID 24239089 DOI: 10.1016/J.Sbi.2013.10.003  0.349
2013 Rodrigues JP, Melquiond AS, Karaca E, Trellet M, van Dijk M, van Zundert GC, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AM. Defining the limits of homology modeling in information-driven protein docking. Proteins. 81: 2119-28. PMID 23913867 DOI: 10.1002/Prot.24382  0.806
2013 van der Schot G, Zhang Z, Vernon R, Shen Y, Vranken WF, Baker D, Bonvin AM, Lange OF. Improving 3D structure prediction from chemical shift data. Journal of Biomolecular Nmr. 57: 27-35. PMID 23912841 DOI: 10.1007/S10858-013-9762-6  0.315
2013 Kastritis PL, Bonvin AM. Molecular origins of binding affinity: seeking the Archimedean point. Current Opinion in Structural Biology. 23: 868-77. PMID 23876790 DOI: 10.1016/J.Sbi.2013.07.001  0.642
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.8
2013 Karaca E, Bonvin AM. On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys. Acta Crystallographica. Section D, Biological Crystallography. 69: 683-94. PMID 23633577 DOI: 10.1107/S0907444913007063  0.69
2013 van Dijk M, Visscher KM, Kastritis PL, Bonvin AM. Solvated protein-DNA docking using HADDOCK. Journal of Biomolecular Nmr. 56: 51-63. PMID 23625455 DOI: 10.1007/S10858-013-9734-X  0.666
2013 Trellet M, Melquiond AS, Bonvin AM. A unified conformational selection and induced fit approach to protein-peptide docking. Plos One. 8: e58769. PMID 23516555 DOI: 10.1371/Journal.Pone.0058769  0.81
2013 Alex S, Lange K, Amolo T, Grinstead JS, Haakonsson AK, Szalowska E, Koppen A, Mudde K, Haenen D, Al-Lahham S, Roelofsen H, Houtman R, van der Burg B, Mandrup S, Bonvin AM, et al. Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating peroxisome proliferator-activated receptor γ. Molecular and Cellular Biology. 33: 1303-16. PMID 23339868 DOI: 10.1128/MCB.00858-12  0.726
2013 Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular complexes. Methods (San Diego, Calif.). 59: 372-81. PMID 23267861 DOI: 10.1016/J.Ymeth.2012.12.004  0.709
2013 Kastritis PL, Bonvin AM. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. Journal of the Royal Society, Interface / the Royal Society. 10: 20120835. PMID 23235262 DOI: 10.1098/Rsif.2012.0835  0.687
2013 Kastritis PL, Visscher KM, van Dijk AD, Bonvin AM. Solvated protein-protein docking using Kyte-Doolittle-based water preferences. Proteins. 81: 510-8. PMID 23161727 DOI: 10.1002/Prot.24210  0.617
2012 Wassenaar TA, de Vries S, Bonvin AM, Bekker H. SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions. Journal of Chemical Theory and Computation. 8: 3618-27. PMID 26593007 DOI: 10.1021/ct3000662  0.685
2012 van Dijk M, Wassenaar TA, Bonvin AM. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 8: 3463-72. PMID 26592996 DOI: 10.1021/ct300102d  0.608
2012 Hennig J, de Vries SJ, Hennig KD, Randles L, Walters KJ, Sunnerhagen M, Bonvin AM. MTMDAT-HADDOCK: high-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry. Bmc Structural Biology. 12: 29. PMID 23153250 DOI: 10.1186/1472-6807-12-29  0.538
2012 van Wijk SJ, Melquiond AS, de Vries SJ, Timmers HT, Bonvin AM. Dynamic control of selectivity in the ubiquitination pathway revealed by an ASP to GLU substitution in an intra-molecular salt-bridge network. Plos Computational Biology. 8: e1002754. PMID 23133359 DOI: 10.1371/Journal.Pcbi.1002754  0.793
2012 Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, et al. In support of the BMRB. Nature Structural & Molecular Biology. 19: 854-60. PMID 22955930 DOI: 10.1038/Nsmb.2371  0.746
2012 Weingarth M, Ader C, Melquiond AS, Nand D, Pongs O, Becker S, Bonvin AM, Baldus M. Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations. Biophysical Journal. 103: 29-37. PMID 22828329 DOI: 10.1016/J.Bpj.2012.05.016  0.79
2012 Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. Clustering biomolecular complexes by residue contacts similarity. Proteins. 80: 1810-7. PMID 22489062 DOI: 10.1002/Prot.24078  0.783
2012 Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, ... ... Bonvin AM, et al. Blind testing of routine, fully automated determination of protein structures from NMR data. Structure (London, England : 1993). 20: 227-36. PMID 22325772 DOI: 10.1016/J.Str.2012.01.002  0.617
2012 Kastritis PL, van Dijk AD, Bonvin AM. Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach. Methods in Molecular Biology (Clifton, N.J.). 819: 355-74. PMID 22183547 DOI: 10.1007/978-1-61779-465-0_22  0.664
2012 Rodrigues J, Schmitz C, Trellet M, Melquiond A, Bonvin A. Clustering biomolecular structures by residue contact similarity F1000research. 3. DOI: 10.7490/F1000Research.1090095.1  0.767
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Bonvin AM, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.813
2011 Stratmann D, Boelens R, Bonvin AM. Quantitative use of chemical shifts for the modeling of protein complexes. Proteins. 79: 2662-70. PMID 21744392 DOI: 10.1002/Prot.23090  0.653
2011 Schmitz C, Bonvin AM. Protein-protein HADDocking using exclusively pseudocontact shifts. Journal of Biomolecular Nmr. 50: 263-6. PMID 21626213 DOI: 10.1007/s10858-011-9514-4  0.804
2011 Wu AM, Singh T, Liu JH, André S, Lensch M, Siebert HC, Krzeminski M, Bonvin AM, Kaltner H, Wu JH, Gabius HJ. Adhesion/growth-regulatory galectins: insights into their ligand selectivity using natural glycoproteins and glycotopes. Advances in Experimental Medicine and Biology. 705: 117-41. PMID 21618107 DOI: 10.1007/978-1-4419-7877-6_7  0.679
2011 Fiamegos YC, Kastritis PL, Exarchou V, Han H, Bonvin AM, Vervoort J, Lewis K, Hamblin MR, Tegos GP. Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria. Plos One. 6: e18127. PMID 21483731 DOI: 10.1371/Journal.Pone.0018127  0.587
2011 Karaca E, Bonvin AM. A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. Structure (London, England : 1993). 19: 555-65. PMID 21481778 DOI: 10.1016/J.Str.2011.01.014  0.717
2011 de Vries SJ, Bonvin AM. CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK. Plos One. 6: e17695. PMID 21464987 DOI: 10.1371/journal.pone.0017695  0.538
2011 Koehler C, Carlier L, Veggi D, Balducci E, Di Marcello F, Ferrer-Navarro M, Pizza M, Daura X, Soriani M, Boelens R, Bonvin AM. Structural and biochemical characterization of NarE, an iron-containing ADP-ribosyltransferase from Neisseria meningitidis. The Journal of Biological Chemistry. 286: 14842-51. PMID 21367854 DOI: 10.1074/Jbc.M110.193623  0.797
2011 Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J. A structure-based benchmark for protein-protein binding affinity. Protein Science : a Publication of the Protein Society. 20: 482-91. PMID 21213247 DOI: 10.1002/Pro.580  0.688
2011 Neumoin A, Leonchiks A, Petit P, Vuillard L, Pizza M, Soriani M, Boelens R, Bonvin AM. 1H, 13C and 15N assignment of the GNA1946 outer membrane lipoprotein from Neisseria meningitidis. Biomolecular Nmr Assignments. 5: 135-8. PMID 21188561 DOI: 10.1007/S12104-010-9285-Y  0.572
2011 Krzeminski M, Singh T, André S, Lensch M, Wu AM, Bonvin AM, Gabius HJ. Human galectin-3 (Mac-2 antigen): defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region. Biochimica Et Biophysica Acta. 1810: 150-61. PMID 21070836 DOI: 10.1016/j.bbagen.2010.11.001  0.724
2011 Carlier L, Koehler C, Veggi D, Pizza M, Soriani M, Boelens R, Bonvin AM. NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitidis. Biomolecular Nmr Assignments. 5: 35-8. PMID 20737254 DOI: 10.1007/S12104-010-9261-6  0.79
2010 Nicastro G, Todi SV, Karaca E, Bonvin AM, Paulson HL, Pastore A. Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3. Plos One. 5: e12430. PMID 20865150 DOI: 10.1371/Journal.Pone.0012430  0.695
2010 de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM. Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions. Proteins. 78: 3242-9. PMID 20718048 DOI: 10.1002/Prot.22814  0.808
2010 de Vries SJ, van Dijk M, Bonvin AM. The HADDOCK web server for data-driven biomolecular docking. Nature Protocols. 5: 883-97. PMID 20431534 DOI: 10.1038/nprot.2010.32  0.519
2010 Kastritis PL, Bonvin AM. Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. Journal of Proteome Research. 9: 2216-25. PMID 20329755 DOI: 10.1021/Pr9009854  0.668
2010 Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Molecular & Cellular Proteomics : McP. 9: 1784-94. PMID 20305088 DOI: 10.1074/Mcp.M000051-Mcp201  0.822
2010 Bonvin AM, Rosato A, Wassenaar TA. The eNMR platform for structural biology. Journal of Structural and Functional Genomics. 11: 1-8. PMID 20229048 DOI: 10.1007/s10969-010-9084-9  0.626
2010 Krzeminski M, Loth K, Boelens R, Bonvin AM. SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes. Bmc Bioinformatics. 11: 51. PMID 20102599 DOI: 10.1186/1471-2105-11-51  0.818
2009 Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Montelione GT, ... ... Bonvin AM, et al. CASD-NMR: critical assessment of automated structure determination by NMR. Nature Methods. 6: 625-6. PMID 19718014 DOI: 10.1038/Nmeth0909-625  0.621
2009 van Wijk SJ, de Vries SJ, Kemmeren P, Huang A, Boelens R, Bonvin AM, Timmers HT. A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. Molecular Systems Biology. 5: 295. PMID 19690564 DOI: 10.1038/Msb.2009.55  0.647
2009 Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R. Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. Journal of Molecular Biology. 390: 478-89. PMID 19450607 DOI: 10.1016/J.Jmb.2009.05.022  0.715
2009 Stockner T, de Vries SJ, Bonvin AM, Ecker GF, Chiba P. Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexibility of the transmembrane domains. The Febs Journal. 276: 964-72. PMID 19215299 DOI: 10.1111/J.1742-4658.2008.06832.X  0.464
2009 Repanas K, Fuentes G, Cohen SX, Bonvin AM, Perrakis A. Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease. Proteins. 74: 917-28. PMID 18767160 DOI: 10.1002/Prot.22201  0.568
2009 Krzeminski M, Fuentes G, Boelens R, Bonvin AM. MINOES: a new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states. Application to Delta25-PYP. Proteins. 74: 895-904. PMID 18704926 DOI: 10.1002/Prot.22197  0.808
2008 de Vries SJ, Bonvin AM. How proteins get in touch: interface prediction in the study of biomolecular complexes. Current Protein & Peptide Science. 9: 394-406. PMID 18691126 DOI: 10.2174/138920308785132712  0.52
2008 Fuentes G, van Dijk AD, Bonvin AM. Nuclear magnetic resonance-based modeling and refinement of protein three-dimensional structures and their complexes. Methods in Molecular Biology (Clifton, N.J.). 443: 229-55. PMID 18446291 DOI: 10.1007/978-1-59745-177-2_13  0.626
2007 Gelis I, Bonvin AM, Keramisanou D, Koukaki M, Gouridis G, Karamanou S, Economou A, Kalodimos CG. Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR. Cell. 131: 756-69. PMID 18022369 DOI: 10.1016/J.Cell.2007.09.039  0.605
2007 de Vries SJ, van Dijk AD, Krzeminski M, van Dijk M, Thureau A, Hsu V, Wassenaar T, Bonvin AM. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins. 69: 726-33. PMID 17803234 DOI: 10.1002/Prot.21723  0.804
2007 van Dijk AD, Ciofi-Baffoni S, Banci L, Bertini I, Boelens R, Bonvin AM. Modeling protein-protein complexes involved in the cytochrome C oxidase copper-delivery pathway. Journal of Proteome Research. 6: 1530-9. PMID 17338559 DOI: 10.1021/Pr060651F  0.644
2007 Wu AM, Singh T, Liu JH, Krzeminski M, Russwurm R, Siebert HC, Bonvin AM, André S, Gabius HJ. Activity-structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16. Glycobiology. 17: 165-84. PMID 17060369 DOI: 10.1093/glycob/cwl062  0.754
2006 Sibille N, Favier A, Azuaga AI, Ganshaw G, Bott R, Bonvin AM, Boelens R, van Nuland NA. Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase. Protein Science : a Publication of the Protein Society. 15: 1915-27. PMID 16823035 DOI: 10.1110/Ps.062213706  0.583
2006 van Dijk M, van Dijk AD, Hsu V, Boelens R, Bonvin AM. Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Research. 34: 3317-25. PMID 16820531 DOI: 10.1093/Nar/Gkl412  0.795
2006 Langedijk JP, Fuentes G, Boshuizen R, Bonvin AM. Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in transmissible spongiform encephalopathies. Journal of Molecular Biology. 360: 907-20. PMID 16782127 DOI: 10.1016/J.Jmb.2006.05.042  0.536
2006 de Vries SJ, Bonvin AM. Intramolecular surface contacts contain information about protein-protein interface regions. Bioinformatics (Oxford, England). 22: 2094-8. PMID 16766554 DOI: 10.1093/bioinformatics/btl275  0.48
2006 AB E, Pugh DJ, Kaptein R, Boelens R, Bonvin AM. Direct use of unassigned resonances in NMR structure calculations with proxy residues. Journal of the American Chemical Society. 128: 7566-71. PMID 16756312 DOI: 10.1021/Ja058504Q  0.747
2006 van Dijk AD, Kaptein R, Boelens R, Bonvin AM. Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking. Journal of Biomolecular Nmr. 34: 237-44. PMID 16645814 DOI: 10.1007/S10858-006-0024-8  0.759
2006 Bonvin AM. Flexible protein-protein docking. Current Opinion in Structural Biology. 16: 194-200. PMID 16488145 DOI: 10.1016/  0.35
2006 de Vries SJ, van Dijk AD, Bonvin AM. WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins. 63: 479-89. PMID 16450362 DOI: 10.1002/prot.20842  0.546
2006 Kamphuis MB, Bonvin AM, Monti MC, Lemonnier M, Muñoz-Gómez A, van den Heuvel RH, Díaz-Orejas R, Boelens R. Model for RNA binding and the catalytic site of the RNase Kid of the bacterial parD toxin-antitoxin system. Journal of Molecular Biology. 357: 115-26. PMID 16413033 DOI: 10.1016/J.Jmb.2005.12.033  0.58
2006 Grinstead JS, Hsu ST, Laan W, Bonvin AM, Hellingwerf KJ, Boelens R, Kaptein R. The solution structure of the AppA BLUF domain: insight into the mechanism of light-induced signaling. Chembiochem : a European Journal of Chemical Biology. 7: 187-93. PMID 16323221 DOI: 10.1002/Cbic.200500270  0.78
2005 Fuentes G, Nederveen AJ, Kaptein R, Boelens R, Bonvin AM. Describing partially unfolded states of proteins from sparse NMR data. Journal of Biomolecular Nmr. 33: 175-86. PMID 16331422 DOI: 10.1007/S10858-005-3207-9  0.799
2005 Bonvin AM, Boelens R, Kaptein R. NMR analysis of protein interactions. Current Opinion in Chemical Biology. 9: 501-8. PMID 16122968 DOI: 10.1016/J.Cbpa.2005.08.011  0.781
2005 Kopke Salinas R, Folkers GE, Bonvin AM, Das D, Boelens R, Kaptein R. Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that mimics the gal repressor. Chembiochem : a European Journal of Chemical Biology. 6: 1628-37. PMID 16094693 DOI: 10.1002/Cbic.200500049  0.765
2005 Doreleijers JF, Nederveen AJ, Vranken W, Lin J, Bonvin AM, Kaptein R, Markley JL, Ulrich EL. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. Journal of Biomolecular Nmr. 32: 1-12. PMID 16041478 DOI: 10.1007/S10858-005-2195-0  0.613
2005 van Dijk AD, de Vries SJ, Dominguez C, Chen H, Zhou HX, Bonvin AM. Data-driven docking: HADDOCK's adventures in CAPRI. Proteins. 60: 232-8. PMID 15981252 DOI: 10.1002/Prot.20563  0.831
2005 Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AM. RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins. 59: 662-72. PMID 15822098 DOI: 10.1002/Prot.20408  0.653
2005 van Dijk AD, Boelens R, Bonvin AM. Data-driven docking for the study of biomolecular complexes. The Febs Journal. 272: 293-312. PMID 15654870 DOI: 10.1111/J.1742-4658.2004.04473.X  0.652
2005 Hsu ST, Peter C, van Gunsteren WF, Bonvin AM. Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation. Biophysical Journal. 88: 15-24. PMID 15489307 DOI: 10.1529/Biophysj.104.044933  0.431
2004 Houben K, Dominguez C, van Schaik FM, Timmers HT, Bonvin AM, Boelens R. Solution structure of the ubiquitin-conjugating enzyme UbcH5B. Journal of Molecular Biology. 344: 513-26. PMID 15522302 DOI: 10.1016/J.Jmb.2004.09.054  0.788
2004 Hsu ST, Breukink E, Tischenko E, Lutters MA, de Kruijff B, Kaptein R, Bonvin AM, van Nuland NA. The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics. Nature Structural & Molecular Biology. 11: 963-7. PMID 15361862 DOI: 10.1038/Nsmb830  0.586
2004 Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science (New York, N.Y.). 305: 386-9. PMID 15256668 DOI: 10.1126/Science.1097064  0.809
2004 Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AM, Vuister GW, Vriend G, Spronk CA. DRESS: a database of REfined solution NMR structures. Proteins. 55: 483-6. PMID 15103611 DOI: 10.1002/Prot.20118  0.59
2004 Dominguez C, Bonvin AM, Winkler GS, van Schaik FM, Timmers HT, Boelens R. Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure (London, England : 1993). 12: 633-44. PMID 15062086 DOI: 10.1016/J.Str.2004.03.004  0.819
2004 van Drogen-Petit A, Zwahlen C, Peter M, Bonvin AM. Insight into molecular interactions between two PB1 domains. Journal of Molecular Biology. 336: 1195-210. PMID 15037079 DOI: 10.1016/J.Jmb.2003.12.062  0.336
2004 Hsu S, Breukink E, Tischenko E, Lutters M, Kruijff Bd, Kaptein R, Bonvin A, Nuland Nv. The pyrophosphate cage: the structure of the nisin/lipid II complex provides a blueprint for novel antibiotics Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb1Uzt/Pdb  0.785
2003 Koharudin LM, Bonvin AM, Kaptein R, Boelens R. Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 163: 228-35. PMID 12914838 DOI: 10.1016/S1090-7807(03)00149-6  0.751
2003 Stockner T, Sterk H, Kaptein R, Bonvin AM. Molecular dynamics studies of a molecular switch in the glucocorticoid receptor. Journal of Molecular Biology. 328: 325-34. PMID 12691744 DOI: 10.1016/S0022-2836(03)00316-4  0.635
2003 Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, Vriend G. The precision of NMR structure ensembles revisited. Journal of Biomolecular Nmr. 25: 225-34. PMID 12652134 DOI: 10.1023/A:1022819716110  0.577
2003 Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society. 125: 1731-7. PMID 12580598 DOI: 10.1021/Ja026939X  0.831
2003 Hsu ST, Breukink E, Bierbaum G, Sahl HG, de Kruijff B, Kaptein R, van Nuland NA, Bonvin AM. NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles. Conformational changes are a key to antimicrobial activity. The Journal of Biological Chemistry. 278: 13110-7. PMID 12562773 DOI: 10.1074/Jbc.M211144200  0.604
2003 Hsu S, Breukink E, Bierbaum G, Sahl H, Kruijff Bd, Kaptein R, Nuland Nv, Bonvin A. NMR solution structure of type-B lantibiotics mersacidin in DPC micelles Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb1Mqy/Pdb  0.777
2003 Hsu S, Breukink E, Bierbaum G, Sahl H, Kruijff Bd, Kaptein R, Nuland Nv, Bonvin A. NMR solution structure of type-B lantibiotics mersacidin in MeOH/H2O mixture Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5581  0.778
2003 Hsu S, Breukink E, Bierbaum G, Sahl H, Kruijff Bd, Kaptein R, Nuland Nv, Bonvin A. NMR solution structure of type-B lantibiotics mersacidin bound to lipid II in DPC micelles Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5580  0.776
2002 Singh S, Folkers GE, Bonvin AM, Boelens R, Wechselberger R, Niztayev A, Kaptein R. Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli. The Embo Journal. 21: 6257-66. PMID 12426397 DOI: 10.1093/Emboj/Cdf627  0.739
2002 Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R, Boelens R, Kaptein R. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. The Embo Journal. 21: 2866-76. PMID 12065400 DOI: 10.1093/Emboj/Cdf318  0.8
2002 Hsu ST, Breukink E, de Kruijff B, Kaptein R, Bonvin AM, van Nuland NA. Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles. Biochemistry. 41: 7670-6. PMID 12056898 DOI: 10.1021/Bi025679T  0.591
2002 D'Amelio N, Bonvin AM, Czisch M, Barker P, Kaptein R. The C terminus of apocytochrome b562 undergoes fast motions and slow exchange among ordered conformations resembling the folded state. Biochemistry. 41: 5505-14. PMID 11969411 DOI: 10.1021/Bi011863N  0.602
2002 Kalodimos C, Bonvin A, Salinas R, Wechselberger R, Boelens R, Kaptein R. Assignment of lac repressor headpiece complexed of its natural operator Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5345  0.772
2002 D'Amelio N, Bonvin A, Czisch M, Barker P, Kaptein R. 1Ha and 13Ca, 13Cb shifts of apocytochrome b562 at pH 5.1 (temperature 293 K) Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr4767  0.545
2001 Bonvin AM, Houben K, Guenneugues M, Kaptein R, Boelens R. Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC'). Journal of Biomolecular Nmr. 21: 221-33. PMID 11775739 DOI: 10.1023/A:1012935005256  0.736
2000 van Tilborg PJ, Czisch M, Mulder FA, Folkers GE, Bonvin AM, Nair M, Boelens R, Kaptein R. Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site. Biochemistry. 39: 8747-57. PMID 10913286 DOI: 10.1021/Bi991550G  0.796
2000 Melacini G, Bonvin AM, Goodman M, Boelens R, Kaptein R. Hydration dynamics of the collagen triple helix by NMR. Journal of Molecular Biology. 300: 1041-9. PMID 10903852 DOI: 10.1006/Jmbi.2000.3919  0.784
2000 van Beest M, Dooijes D, van De Wetering M, Kjaerulff S, Bonvin A, Nielsen O, Clevers H. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs. The Journal of Biological Chemistry. 275: 27266-73. PMID 10867006 DOI: 10.1074/Jbc.M004102200  0.333
2000 Bonvin AM, van Gunsteren WF. beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. Journal of Molecular Biology. 296: 255-68. PMID 10656830 DOI: 10.1006/jmbi.1999.3446  0.431
1999 Spronk CA, Bonvin AM, Radha PK, Melacini G, Boelens R, Kaptein R. The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator. Structure (London, England : 1993). 7: 1483-92. PMID 10647179 DOI: 10.1016/S0969-2126(00)88339-2  0.809
1998 Bonvin AM, Sunnerhagen M, Otting G, van Gunsteren WF. Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. Journal of Molecular Biology. 282: 859-73. PMID 9743632 DOI: 10.1006/jmbi.1998.2034  0.42
1996 Slijper M, Bonvin AM, Boelens R, Kaptein R. Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator. Journal of Molecular Biology. 259: 761-73. PMID 8683581 DOI: 10.1006/Jmbi.1996.0356  0.76
1995 van Tilborg MA, Bonvin AM, Hård K, Davis AL, Maler B, Boelens R, Yamamoto KR, Kaptein R. Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. Journal of Molecular Biology. 247: 689-700. PMID 7723024 DOI: 10.1016/S0022-2836(05)80148-2  0.752
1995 Bonvin AM, Brünger AT. Conformational variability of solution nuclear magnetic resonance structures. Journal of Molecular Biology. 250: 80-93. PMID 7602599  0.306
1994 Bonvin AM, Boelens R, Kaptein R. Time- and ensemble-averaged direct NOE restraints. Journal of Biomolecular Nmr. 4: 143-9. PMID 22911161 DOI: 10.1007/Bf00178343  0.741
1994 Bonvin AM, Vis H, Breg JN, Burgering MJ, Boelens R, Kaptein R. Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations. Journal of Molecular Biology. 236: 328-41. PMID 8107113 DOI: 10.1006/Jmbi.1994.1138  0.751
1993 Bonvin AM, Rullmann JA, Lamerichs RM, Boelens R, Kaptein R. "Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin. Proteins. 15: 385-400. PMID 8460109 DOI: 10.1002/Prot.340150406  0.748
1993 Knegtel RM, Boelens R, Ganadu ML, George AV, Katahira M, Bonvin AM, Eib D, van der Saag PT, Kaptein R. NMR studies of the human retinoic acid receptor-beta DNA-binding domain. Metal coordination and three-dimensional structure. Annals of the New York Academy of Sciences. 684: 49-62. PMID 8391240 DOI: 10.1111/J.1749-6632.1993.Tb32270.X  0.712
1993 Knegtel RM, Katahira M, Schilthuis JG, Bonvin AM, Boelens R, Eib D, van der Saag PT, Kaptein R. The solution structure of the human retinoic acid receptor-beta DNA-binding domain. Journal of Biomolecular Nmr. 3: 1-17. PMID 8383553 DOI: 10.1007/Bf00242472  0.732
1991 Bonvin AM, Boelens R, Kaptein R. Direct NOE refinement of biomolecular structures using 2D NMR data. Journal of Biomolecular Nmr. 1: 305-9. PMID 1841701 DOI: 10.1007/Bf01875523  0.731
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