| Year |
Citation |
Score |
| 2023 |
van der Krift F, Zijlmans DW, Shukla R, Javed A, Koukos PI, Schwarz LL, Timmermans-Sprang EP, Maas PE, Gahtory D, van den Nieuwboer M, Mol JA, Strous GJ, Bonvin AM, van der Stelt M, Veldhuizen EJ, et al. A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance. Life Science Alliance. 6. PMID 37591722 DOI: 10.26508/lsa.202302058 |
0.702 |
|
| 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 |
0.643 |
|
| 2019 |
Morris C, Andreetto P, Banci L, Bonvin AM, Chojnowski G, Cano Ld, Carazo JM, Conesa P, Daenke S, Damaskos G, Giachetti A, Haley NE, Hekkelman ML, Heuser P, Joosten RP, et al. West-Life: A Virtual Research Environment for structural biology Journal of Structural Biology: X. 1: 100006. DOI: 10.1016/j.yjsbx.2019.100006 |
0.268 |
|
| 2019 |
Bonvin AM. High-Resolution, Integrative Modelling of Biomolecular Complexes Biophysical Journal. 116: 329a. DOI: 10.1016/j.bpj.2018.11.1787 |
0.3 |
|
| 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 |
0.794 |
|
| 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 |
0.672 |
|
| 2016 |
Felix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN. Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF. Nature Communications. 7: 13228. PMID 27819269 DOI: 10.1038/Ncomms13228 |
0.298 |
|
| 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 |
0.778 |
|
| 2016 |
Grinter R, Josts I, Mosbahi K, Roszak AW, Cogdell RJ, Bonvin AM, Milner JJ, Kelly SM, Byron O, Smith BO, Walker D. Structure of the bacterial plant-ferredoxin receptor FusA. Nature Communications. 7: 13308. PMID 27796364 DOI: 10.1038/ncomms13308 |
0.261 |
|
| 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 |
0.812 |
|
| 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 |
0.674 |
|
| 2016 |
van Zundert GC, Bonvin AM. Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. Journal of Structural Biology. PMID 27318041 DOI: 10.1016/j.jsb.2016.06.011 |
0.318 |
|
| 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 |
0.802 |
|
| 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 |
0.546 |
|
| 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 |
0.49 |
|
| 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 |
0.81 |
|
| 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 |
0.672 |
|
| 2016 |
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, ... Bonvin AM, et al. Data publication with the structural biology data grid supports live analysis. Nature Communications. 7: 10882. PMID 26947396 DOI: 10.1038/Ncomms10882 |
0.309 |
|
| 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 |
0.508 |
|
| 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 |
0.788 |
|
| 2016 |
Zhang R, Eckert T, Lutteke T, Hanstein S, Scheidig A, Bonvin AM, Nifantiev NE, Kozar T, Schauer R, Enani MA, Siebert HC. Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to Contact Molecules on Pathogen Surfaces. Current Topics in Medicinal Chemistry. 16: 89-98. PMID 26139116 |
0.328 |
|
| 2016 |
Matser V, Brooksbank C, Apostolov R, Carter A, Bonvin A, Abraham M, Ippoliti E. Applying competency profiling of user groups to develop a training programme in Computational Biomolecular Research F1000research. 5. DOI: 10.7490/F1000Research.1113076.1 |
0.327 |
|
| 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 |
0.748 |
|
| 2015 |
Kalia M, Willkomm S, Claussen JC, Restle T, Bonvin AM. Novel Insights into Guide RNA 5'-Nucleoside/Tide Binding by Human Argonaute 2. International Journal of Molecular Sciences. 17. PMID 26712743 DOI: 10.3390/ijms17010022 |
0.243 |
|
| 2015 |
Deplazes E, Davies J, Bonvin AM, King GF, Mark AE. On the Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a. Journal of Chemical Information and Modeling. PMID 26642380 DOI: 10.1021/Acs.Jcim.5B00529 |
0.4 |
|
| 2015 |
Bonvin AM, Keskin O. Editorial overview: Protein-protein interactions. Current Opinion in Structural Biology. PMID 26631291 DOI: 10.1016/J.Sbi.2015.11.004 |
0.357 |
|
| 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 |
0.601 |
|
| 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 |
0.784 |
|
| 2015 |
Marino F, Bern M, Mommen GP, Leney AC, van Gaans-van den Brink JA, Bonvin AM, Becker C, van Els CA, Heck AJ. Extended O-GlcNAc on HLA Class-I-Bound Peptides. Journal of the American Chemical Society. 137: 10922-5. PMID 26280087 DOI: 10.1021/Jacs.5B06586 |
0.242 |
|
| 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 |
0.833 |
|
| 2015 |
Duarte AM, Psomopoulos FE, Blanchet C, Bonvin AM, Corpas M, Franc A, Jimenez RC, de Lucas JM, Nyrönen T, Sipos G, Suhr SB. Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis. Frontiers in Genetics. 6: 197. PMID 26157454 DOI: 10.3389/fgene.2015.00197 |
0.26 |
|
| 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 |
0.587 |
|
| 2015 |
Brewer KD, Bacaj T, Cavalli A, Camilloni C, Swarbrick JD, Liu J, Zhou A, Zhou P, Barlow N, Xu J, Seven AB, Prinslow EA, Voleti R, Häussinger D, Bonvin AM, et al. Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution. Nature Structural & Molecular Biology. 22: 555-64. PMID 26030874 DOI: 10.1038/Nsmb.3035 |
0.382 |
|
| 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 |
0.656 |
|
| 2015 |
van Zundert GC, Bonvin AM. DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. Bioinformatics (Oxford, England). 31: 3222-4. PMID 26026169 DOI: 10.1093/bioinformatics/btv333 |
0.289 |
|
| 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 |
0.528 |
|
| 2015 |
Kaplan M, Cukkemane A, van Zundert GC, Narasimhan S, Daniëls M, Mance D, Waksman G, Bonvin AM, Fronzes R, Folkers GE, Baldus M. Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR. Nature Methods. PMID 25984698 DOI: 10.1038/Nmeth.3406 |
0.407 |
|
| 2015 |
van der Schot G, Bonvin AM. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. Journal of Biomolecular Nmr. 62: 497-502. PMID 25982706 DOI: 10.1007/s10858-015-9942-7 |
0.361 |
|
| 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 |
0.807 |
|
| 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 |
0.783 |
|
| 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 |
0.645 |
|
| 2015 |
Vangone A, Bonvin AM. Author response: Contacts-based prediction of binding affinity in protein–protein complexes Elife. DOI: 10.7554/Elife.07454.018 |
0.733 |
|
| 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 |
0.746 |
|
| 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 |
0.64 |
|
| 2014 |
Rey M, Sarpe V, Burns KM, Buse J, Baker CA, van Dijk M, Wordeman L, Bonvin AM, Schriemer DC. Mass spec studio for integrative structural biology. Structure (London, England : 1993). 22: 1538-48. PMID 25242457 DOI: 10.1016/J.Str.2014.08.013 |
0.32 |
|
| 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 |
0.818 |
|
| 2014 |
van Ingen H, Bonvin AM. Information-driven modeling of large macromolecular assemblies using NMR data. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 241: 103-14. PMID 24656083 DOI: 10.1016/j.jmr.2013.10.021 |
0.392 |
|
| 2014 |
Rodrigues JP, Bonvin AM. Integrative computational modeling of protein interactions. The Febs Journal. 281: 1988-2003. PMID 24588898 DOI: 10.1111/febs.12771 |
0.634 |
|
| 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 |
0.456 |
|
| 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 |
0.813 |
|
| 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 |
0.807 |
|
| 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 |
0.797 |
|
| 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 |
0.561 |
|
| 2014 |
Kalia M, Willkomm S, Christian Claussen J, Bonvin AM, Restle T. A Single Inter-Domain Salt Bridge within the Human Argonaute 2 Protein Crucially Affects Protein Folding and Consequently Enzymatic Activity Biophysical Journal. 106: 26a. DOI: 10.1016/j.bpj.2013.11.198 |
0.344 |
|
| 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 |
0.547 |
|
| 2013 |
Varney KM, Bonvin AM, Pazgier M, Malin J, Yu W, Ateh E, Oashi T, Lu W, Huang J, Diepeveen-de Buin M, Bryant J, Breukink E, Mackerell AD, de Leeuw EP. Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. Plos Pathogens. 9: e1003732. PMID 24244161 DOI: 10.1371/Journal.Ppat.1003732 |
0.299 |
|
| 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 |
0.447 |
|
| 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 |
0.809 |
|
| 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 |
0.428 |
|
| 2013 |
van der Cruijsen EA, Nand D, Weingarth M, Prokofyev A, Hornig S, Cukkemane AA, Bonvin AM, Becker S, Hulse RE, Perozo E, Pongs O, Baldus M. Importance of lipid-pore loop interface for potassium channel structure and function. Proceedings of the National Academy of Sciences of the United States of America. 110: 13008-13. PMID 23882077 DOI: 10.1073/Pnas.1305563110 |
0.254 |
|
| 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 |
0.766 |
|
| 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 |
0.689 |
|
| 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 |
0.782 |
|
| 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 |
0.812 |
|
| 2013 |
Lutje Hulsik D, Liu YY, Strokappe NM, Battella S, El Khattabi M, McCoy LE, Sabin C, Hinz A, Hock M, Macheboeuf P, Bonvin AM, Langedijk JP, Davis D, Forsman Quigley A, Aasa-Chapman MM, et al. A gp41 MPER-specific llama VHH requires a hydrophobic CDR3 for neutralization but not for antigen recognition. Plos Pathogens. 9: e1003202. PMID 23505368 DOI: 10.1371/Journal.Ppat.1003202 |
0.242 |
|
| 2013 |
Weingarth M, Prokofyev A, van der Cruijsen EA, Nand D, Bonvin AM, Pongs O, Baldus M. Structural determinants of specific lipid binding to potassium channels. Journal of the American Chemical Society. 135: 3983-8. PMID 23425320 DOI: 10.1021/Ja3119114 |
0.326 |
|
| 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 |
0.742 |
|
| 2013 |
Dagil R, O'Shea C, Nykjær A, Bonvin AM, Kragelund BB. Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin. The Journal of Biological Chemistry. 288: 4424-35. PMID 23275343 DOI: 10.1074/jbc.M112.434159 |
0.379 |
|
| 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 |
0.707 |
|
| 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 |
0.796 |
|
| 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 |
0.75 |
|
| 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 |
0.705 |
|
| 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 |
0.638 |
|
| 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 |
0.594 |
|
| 2012 |
Gradmann S, Ader C, Heinrich I, Nand D, Dittmann M, Cukkemane A, van Dijk M, Bonvin AM, Engelhard M, Baldus M. Rapid prediction of multi-dimensional NMR data sets. Journal of Biomolecular Nmr. 54: 377-87. PMID 23143278 DOI: 10.1007/S10858-012-9681-Y |
0.364 |
|
| 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 |
0.795 |
|
| 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 |
0.747 |
|
| 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 |
0.791 |
|
| 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 |
0.784 |
|
| 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 |
0.652 |
|
| 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 |
0.782 |
|
| 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 |
0.769 |
|
| 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 |
0.81 |
|
| 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 |
0.683 |
|
| 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 |
0.814 |
|
| 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 |
0.7 |
|
| 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 |
0.731 |
|
| 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 |
0.592 |
|
| 2011 |
Escobar-Cabrera E, Okon M, Lau DK, Dart CF, Bonvin AM, McIntosh LP. Characterizing the N- and C-terminal Small ubiquitin-like modifier (SUMO)-interacting motifs of the scaffold protein DAXX. The Journal of Biological Chemistry. 286: 19816-29. PMID 21383010 DOI: 10.1074/Jbc.M111.231647 |
0.33 |
|
| 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 |
0.798 |
|
| 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 |
0.796 |
|
| 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 |
0.61 |
|
| 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 |
0.742 |
|
| 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 |
0.791 |
|
| 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 |
0.696 |
|
| 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 |
0.807 |
|
| 2010 |
Schneider T, Kruse T, Wimmer R, Wiedemann I, Sass V, Pag U, Jansen A, Nielsen AK, Mygind PH, Raventós DS, Neve S, Ravn B, Bonvin AM, De Maria L, Andersen AS, et al. Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II. Science (New York, N.Y.). 328: 1168-72. PMID 20508130 DOI: 10.1126/Science.1185723 |
0.32 |
|
| 2010 |
van Dijk M, Bonvin AM. Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. Nucleic Acids Research. 38: 5634-47. PMID 20466807 DOI: 10.1093/nar/gkq222 |
0.389 |
|
| 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 |
0.574 |
|
| 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 |
0.784 |
|
| 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 |
0.654 |
|
| 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 |
0.823 |
|
| 2010 |
Kobayashi M, Ab E, Bonvin AM, Siegal G. Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex. The Journal of Biological Chemistry. 285: 10087-97. PMID 20081198 DOI: 10.1074/jbc.M109.054106 |
0.359 |
|
| 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 |
0.655 |
|
| 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 |
0.673 |
|
| 2009 |
Eggink D, Langedijk JP, Bonvin AM, Deng Y, Lu M, Berkhout B, Sanders RW. Detailed mechanistic insights into HIV-1 sensitivity to three generations of fusion inhibitors. The Journal of Biological Chemistry. 284: 26941-50. PMID 19617355 DOI: 10.1074/jbc.M109.004416 |
0.245 |
|
| 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 |
0.733 |
|
| 2009 |
van Dijk M, Bonvin AM. 3D-DART: a DNA structure modelling server. Nucleic Acids Research. 37: W235-9. PMID 19417072 DOI: 10.1093/nar/gkp287 |
0.346 |
|
| 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 |
0.528 |
|
| 2009 |
Rutten L, Mannie JP, Stead CM, Raetz CR, Reynolds CM, Bonvin AM, Tommassen JP, Egmond MR, Trent MS, Gros P. Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium. Proceedings of the National Academy of Sciences of the United States of America. 106: 1960-4. PMID 19174515 DOI: 10.1073/Pnas.0813064106 |
0.287 |
|
| 2009 |
Jung S, Dingley AJ, Augustin R, Anton-Erxleben F, Stanisak M, Gelhaus C, Gutsmann T, Hammer MU, Podschun R, Bonvin AM, Leippe M, Bosch TC, Grötzinger J. Hydramacin-1, structure and antibacterial activity of a protein from the basal metazoan Hydra. The Journal of Biological Chemistry. 284: 1896-905. PMID 19019828 DOI: 10.1074/Jbc.M804713200 |
0.389 |
|
| 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 |
0.609 |
|
| 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 |
Arnusch CJ, Bonvin AM, Verel AM, Jansen WT, Liskamp RM, de Kruijff B, Pieters RJ, Breukink E. The vancomycin-nisin(1-12) hybrid restores activity against vancomycin resistant Enterococci. Biochemistry. 47: 12661-3. PMID 18989934 DOI: 10.1021/Bi801597B |
0.255 |
|
| 2008 |
Sanders RW, Hsu ST, van Anken E, Liscaljet IM, Dankers M, Bontjer I, Land A, Braakman I, Bonvin AM, Berkhout B. Evolution rescues folding of human immunodeficiency virus-1 envelope glycoprotein GP120 lacking a conserved disulfide bond. Molecular Biology of the Cell. 19: 4707-16. PMID 18753405 DOI: 10.1091/Mbc.E08-07-0670 |
0.273 |
|
| 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 |
0.579 |
|
| 2008 |
van Dijk M, Bonvin AM. A protein-DNA docking benchmark. Nucleic Acids Research. 36: e88. PMID 18583363 DOI: 10.1093/nar/gkn386 |
0.356 |
|
| 2008 |
Corrêa F, Salinas RK, Bonvin AM, Farah CS. Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex. Proteins. 73: 902-17. PMID 18536019 DOI: 10.1002/prot.22116 |
0.374 |
|
| 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 |
0.66 |
|
| 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 |
0.636 |
|
| 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 |
0.805 |
|
| 2007 |
Tomaselli S, Ragona L, Zetta L, Assfalg M, Ferranti P, Longhi R, Bonvin AM, Molinari H. NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids. Proteins. 69: 177-91. PMID 17607743 DOI: 10.1002/prot.21517 |
0.406 |
|
| 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 |
0.677 |
|
| 2007 |
Jeninga EH, van Beekum O, van Dijk AD, Hamers N, Hendriks-Stegeman BI, Bonvin AM, Berger R, Kalkhoven E. Impaired peroxisome proliferator-activated receptor gamma function through mutation of a conserved salt bridge (R425C) in familial partial lipodystrophy. Molecular Endocrinology (Baltimore, Md.). 21: 1049-65. PMID 17312272 DOI: 10.1210/me.2006-0485 |
0.289 |
|
| 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 |
0.77 |
|
| 2006 |
Jensen GA, Andersen OM, Bonvin AM, Bjerrum-Bohr I, Etzerodt M, Thøgersen HC, O'Shea C, Poulsen FM, Kragelund BB. Binding site structure of one LRP-RAP complex: implications for a common ligand-receptor binding motif. Journal of Molecular Biology. 362: 700-16. PMID 16938309 DOI: 10.1016/j.jmb.2006.07.013 |
0.359 |
|
| 2006 |
van Dijk AD, Bonvin AM. Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics (Oxford, England). 22: 2340-7. PMID 16899489 DOI: 10.1093/bioinformatics/btl395 |
0.378 |
|
| 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 |
0.621 |
|
| 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 |
0.804 |
|
| 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 |
0.579 |
|
| 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 |
0.543 |
|
| 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 |
0.761 |
|
| 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 |
0.773 |
|
| 2006 |
Rutten L, Geurtsen J, Lambert W, Smolenaers JJ, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, Tommassen J. Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America. 103: 7071-6. PMID 16632613 DOI: 10.1073/Pnas.0509392103 |
0.391 |
|
| 2006 |
Bonvin AM. Flexible protein-protein docking. Current Opinion in Structural Biology. 16: 194-200. PMID 16488145 DOI: 10.1016/j.sbi.2006.02.002 |
0.46 |
|
| 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 |
0.601 |
|
| 2006 |
Tomaselli S, Esposito V, Vangone P, van Nuland NA, Bonvin AM, Guerrini R, Tancredi T, Temussi PA, Picone D. The alpha-to-beta conformational transition of Alzheimer's Abeta-(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of beta conformation seeding. Chembiochem : a European Journal of Chemical Biology. 7: 257-67. PMID 16444756 DOI: 10.1002/cbic.200500223 |
0.306 |
|
| 2006 |
Fuchs PF, Bonvin AM, Bochicchio B, Pepe A, Alix AJ, Tamburro AM. Kinetics and thermodynamics of type VIII beta-turn formation: a CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide. Biophysical Journal. 90: 2745-59. PMID 16443656 DOI: 10.1529/biophysj.105.074401 |
0.243 |
|
| 2006 |
Kamphuis MB, Bonvin AM, Monti MC, Lemonnier M, Muñoz-Gómez A, van den Heuvel RH, DÃaz-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 |
0.619 |
|
| 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 |
0.781 |
|
| 2005 |
Nederveen AJ, Bonvin AM. NMR Relaxation and Internal Dynamics of Ubiquitin from a 0.2 μs MD Simulation. Journal of Chemical Theory and Computation. 1: 363-74. PMID 26641503 DOI: 10.1021/ct0498829 |
0.292 |
|
| 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 |
0.806 |
|
| 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 |
0.794 |
|
| 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 |
0.778 |
|
| 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 |
0.648 |
|
| 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 |
0.832 |
|
| 2005 |
van Dijk AD, Fushman D, Bonvin AM. Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins. 60: 367-81. PMID 15937902 DOI: 10.1002/Prot.20476 |
0.38 |
|
| 2005 |
Lin KF, Liu YN, Hsu ST, Samuel D, Cheng CS, Bonvin AM, Lyu PC. Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean. Biochemistry. 44: 5703-12. PMID 15823028 DOI: 10.1021/bi047608v |
0.367 |
|
| 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 |
0.684 |
|
| 2005 |
Volkov AN, Ferrari D, Worrall JA, Bonvin AM, Ubbink M. The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Protein Science : a Publication of the Protein Society. 14: 799-811. PMID 15689516 DOI: 10.1110/ps.041150205 |
0.267 |
|
| 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 |
0.682 |
|
| 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 |
0.5 |
|
| 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 |
0.789 |
|
| 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 |
0.624 |
|
| 2004 |
Tzakos AG, Fuchs P, van Nuland NA, Troganis A, Tselios T, Deraos S, Matsoukas J, Gerothanassis IP, Bonvin AM. NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: structural implications for the MHC II (I-Au)-peptide complex from docking calculations. European Journal of Biochemistry / Febs. 271: 3399-413. PMID 15291817 DOI: 10.1111/j.1432-1033.2004.04274.x |
0.392 |
|
| 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 |
0.81 |
|
| 2004 |
Hsu ST, Bonvin AM. Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120. Proteins. 55: 582-93. PMID 15103622 DOI: 10.1002/Prot.20061 |
0.31 |
|
| 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 |
0.627 |
|
| 2004 |
Arnesano F, Banci L, Bertini I, Bonvin AM. A docking approach to the study of copper trafficking proteins; interaction between metallochaperones and soluble domains of copper ATPases. Structure (London, England : 1993). 12: 669-76. PMID 15062089 DOI: 10.1016/J.Str.2004.03.006 |
0.4 |
|
| 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 |
0.82 |
|
| 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 |
0.447 |
|
| 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 |
0.786 |
|
| 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 |
0.766 |
|
| 2003 |
Oomen CJ, Hoogerhout P, Bonvin AM, Kuipers B, Brugghe H, Timmermans H, Haseley SR, van Alphen L, Gros P. Immunogenicity of peptide-vaccine candidates predicted by molecular dynamics simulations. Journal of Molecular Biology. 328: 1083-9. PMID 12729743 DOI: 10.1016/S0022-2836(03)00377-2 |
0.313 |
|
| 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 |
0.67 |
|
| 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 |
0.615 |
|
| 2003 |
Tzakos AG, Bonvin AM, Troganis A, Cordopatis P, Amzel ML, Gerothanassis IP, van Nuland NA. On the molecular basis of the recognition of angiotensin II (AII). NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131. European Journal of Biochemistry / Febs. 270: 849-60. PMID 12603318 DOI: 10.1046/j.1432-1033.2003.03441.x |
0.392 |
|
| 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 |
0.833 |
|
| 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 |
0.64 |
|
| 2003 |
Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M. Refinement of protein structures in explicit solvent. Proteins. 50: 496-506. PMID 12557191 DOI: 10.1002/prot.10299 |
0.386 |
|
| 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 |
0.778 |
|
| 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 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 |
0.777 |
|
| 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 |
0.755 |
|
| 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 |
0.801 |
|
| 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 |
0.629 |
|
| 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 |
0.638 |
|
| 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 |
0.583 |
|
| 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 |
0.752 |
|
| 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 |
0.797 |
|
| 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 |
0.794 |
|
| 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 |
0.429 |
|
| 2000 |
Bonvin AM. Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation. European Biophysics Journal : Ebj. 29: 57-60. PMID 10826779 |
0.247 |
|
| 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 |
0.499 |
|
| 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 |
0.811 |
|
| 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 |
0.491 |
|
| 1998 |
Sunnerhagen M, Denisov VP, Venu K, Bonvin AM, Carey J, Halle B, Otting G. Water molecules in DNA recognition I: hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy. Journal of Molecular Biology. 282: 847-58. PMID 9743631 DOI: 10.1006/Jmbi.1998.2033 |
0.305 |
|
| 1996 |
Bonvin AM, Brünger AT. Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? Journal of Biomolecular Nmr. 7: 72-6. PMID 8720833 |
0.32 |
|
| 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 |
0.774 |
|
| 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 |
0.767 |
|
| 1995 |
Bonvin AM, Brünger AT. Conformational variability of solution nuclear magnetic resonance structures. Journal of Molecular Biology. 250: 80-93. PMID 7602599 |
0.419 |
|
| 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 |
0.756 |
|
| 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 |
0.766 |
|
| 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 |
0.762 |
|
| 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 |
0.73 |
|
| 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 |
0.748 |
|
| 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 |
0.747 |
|
| 1990 |
Burghardt I, Di Bari L, Bonvin A, Bodenhausen G. Effects of strong coupling in multiple-quantum-filtered two-dimensional NOE spectroscopy Journal of Magnetic Resonance (1969). 86: 652-656. DOI: 10.1016/0022-2364(90)90044-A |
0.325 |
|
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