Alexandre MJJ Bonvin, Ph.D. - Publications

Affiliations: 
Chemistry Utrecht University, Utrecht, Netherlands 
Area:
Protein-protein interactions, docking
Website:
http://www.nmr.chem.uu.nl/~abonvin/

201 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
2019 Basciu A, Koukos PI, Malloci G, Bonvin AMJJ, Vargiu AV. Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design. PMID 31720895 DOI: 10.1007/s10822-019-00244-6  0.36
2019 Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Bonvin AMJJ, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/prot.25838  0.8
2019 Roel-Touris J, Don CG, V Honorato R, Rodrigues JPGLM, Bonvin AMJJ. Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK. Journal of Chemical Theory and Computation. PMID 31539250 DOI: 10.1021/acs.jctc.9b00310  0.72
2019 Abraham MJ, Apostolov RP, Barnoud J, Bauer P, Blau C, Bonvin AMJJ, Chavent M, Chodera JD, Čondić-Jurkić K, Delemotte L, Grubmüller H, Howard RJ, Jordan EJ, Lindal E, Ollila OHS, et al. Sharing Data from Molecular Simulations. Journal of Chemical Information and Modeling. PMID 31525920 DOI: 10.1021/acs.jcim.9b00665  0.72
2019 Kurkcuoglu Z, Bonvin AMJJ. Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems. Proteins. PMID 31441121 DOI: 10.1002/prot.25802  0.72
2019 Goldbach L, Vermeulen BJA, Caner S, Liu M, Tysoe C, van Gijzel L, Yoshisada R, Trellet M, van Ingen H, Brayer GD, Bonvin AMJJ, Jongkees SAK. Folding Then Binding vs. Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase. Acs Chemical Biology. PMID 31241898 DOI: 10.1021/acschembio.9b00290  0.72
2019 Geng C, Jung Y, Renaud N, Honavar V, Bonvin AMJJ, Xue LC. iScore: A novel graph kernel-based function for scoring protein-protein docking models. Bioinformatics (Oxford, England). PMID 31199455 DOI: 10.1093/bioinformatics/btz496  0.56
2019 Jiménez-García B, Elez K, Koukos PI, Bonvin AMJJ, Vangone A. PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. Bioinformatics (Oxford, England). PMID 31141126 DOI: 10.1093/bioinformatics/btz437  0.56
2019 Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet ME, Xue LC, Bonvin AMJJ. Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinformatics (Oxford, England). 35: 1585-1587. PMID 31051038 DOI: 10.1093/bioinformatics/bty816  0.56
2018 Rodrigues JPGLM, Teixeira JMC, Trellet M, Bonvin AMJJ. pdb-tools: a swiss army knife for molecular structures. F1000research. 7: 1961. PMID 30705752 DOI: 10.12688/f1000research.17456.1  0.72
2018 Broekema MF, Massink MPG, Donato C, de Ligt J, Schaarschmidt J, Borgman A, Schooneman MG, Melchers D, Gerding MN, Houtman R, Bonvin AMJJ, Majithia AR, Monajemi H, van Haaften GW, Soeters MR, et al. Natural helix 9 mutants of PPARγ differently affect its transcriptional activity. Molecular Metabolism. PMID 30595551 DOI: 10.1016/j.molmet.2018.12.005  0.56
2018 Elez K, Bonvin AMJJ, Vangone A. Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification. Bmc Bioinformatics. 19: 438. PMID 30497368 DOI: 10.1186/s12859-018-2414-9  0.56
2018 Geng C, Vangone A, Folkers GE, Xue LC, Bonvin AMJJ. iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations. Proteins. PMID 30417935 DOI: 10.1002/prot.25630  0.96
2018 Koukos PI, Faro I, van Noort CW, Bonvin AMJJ. A Membrane Protein Complex Docking Benchmark. Journal of Molecular Biology. PMID 30414967 DOI: 10.1016/j.jmb.2018.11.005  0.36
2018 Koukos PI, Xue LC, Bonvin AMJJ. Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. Journal of Computer-Aided Molecular Design. PMID 30128928 DOI: 10.1007/s10822-018-0148-4  0.56
2018 Bonvin AMJJ, Karaca E, Kastritis PL, Rodrigues JPGLM. Defining distance restraints in HADDOCK. Nature Protocols. PMID 29942005 DOI: 10.1038/s41596-018-0017-6  0.92
2018 Narasimhan S, Mance D, Pinto C, Weingarth M, Bonvin AMJJ, Baldus M. Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS. Methods in Molecular Biology (Clifton, N.J.). 1688: 111-132. PMID 29151207 DOI: 10.1007/978-1-4939-7386-6_6  0.4
2017 Schaarschmidt J, Monastyrskyy B, Kryshtafovych A, Bonvin AMJJ. Assessment of Contact Predictions in CASP12: Co-Evolution and Deep Learning Coming of Age. Proteins. PMID 29071738 DOI: 10.1002/prot.25407  0.56
2017 Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ. Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. Journal of Computer-Aided Molecular Design. PMID 28831657 DOI: 10.1007/s10822-017-0049-y  0.8
2017 Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gümüş ZH, Costa J, Bonvin AMJJ. SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Scientific Reports. 7: 8007. PMID 28808256 DOI: 10.1038/s41598-017-08321-2  0.72
2017 Karaca E, Rodrigues JPGLM, Graziadei A, Bonvin AMJJ, Carlomagno T. M3: an integrative framework for structure determination of molecular machines. Nature Methods. PMID 28805795 DOI: 10.1038/nmeth.4392  0.92
2017 Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418). Proteins. 85: 1589-1590. PMID 28730688 DOI: 10.1002/prot.25339  0.92
2017 Almeida JG, Preto AJ, Koukos PI, Bonvin AMJJ, Moreira IS. MEMBRANE PROTEINS STRUCTURES: A review on computational modeling tools. Biochimica Et Biophysica Acta. PMID 28716627 DOI: 10.1016/j.bbamem.2017.07.008  0.44
2017 Visscher K, Medeiros-Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M. Supramolecular organization and functional implications of K+ channel clusters in membranes. Angewandte Chemie (International Ed. in English). PMID 28685953 DOI: 10.1002/anie.201705723  0.72
2017 de Bruin RCG, Stam AGM, Vangone A, van Bergen En Henegouwen PMP, Verheul HMW, Sebestyén Z, Kuball J, Bonvin AMJJ, de Gruijl TD, van der Vliet HJ. Correction: Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology (Baltimore, Md. : 1950). 198: 3759. PMID 28416722 DOI: 10.4049/jimmunol.1700317  0.56
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  0.88
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  0.72
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  0.56
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  0.64
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  0.92
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  0.8
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  0.88
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  0.64
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  0.56
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  0.8
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  0.8
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  0.88
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  0.8
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  0.8
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  0.88
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  0.8
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  0.8
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  0.92
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  0.8
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  0.8
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  0.56
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  0.8
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  0.8
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  0.8
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  0.64
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  0.8
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  0.8
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  0.68
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  0.8
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  0.8
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  0.92
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  0.8
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  0.8
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  0.88
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  0.8
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  0.8
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  0.48
2014 Rodrigues JP, Bonvin AM. Integrative computational modeling of protein interactions. The Febs Journal. 281: 1988-2003. PMID 24588898 DOI: 10.1111/febs.12771  0.88
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  0.64
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  0.8
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  0.68
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.92
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  0.8
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  0.8
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  0.8
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  0.8
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  0.4
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  0.92
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  0.8
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  0.8
2013 Dias DM, Rodrigues JPGLM, Domingues NS, Bonvin AMJJ, Castro MMCA. Unveiling the interaction of vanadium compounds with human serum albumin by using 1H STD NMR and computational docking studies European Journal of Inorganic Chemistry. 4619-4627. DOI: 10.1002/ejic.201300419  0.72
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  0.56
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  0.8
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  0.8
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  0.8
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  1
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  0.8
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  0.8
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  0.8
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  0.8
2012 Van Dijk M, Wassenaar TA, Bonvin AMJJ. A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations Journal of Chemical Theory and Computation. 8: 3463-3472. DOI: 10.1021/ct300102d  0.56
2012 Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A, Ferella L, Rosato A, Bertini I, Herrmann T, Jonker HRA, Bagaria A, ... ... Bonvin AMJJ, et al. WeNMR: Structural Biology on the Grid Journal of Grid Computing. 10: 743-767. DOI: 10.1007/s10723-012-9246-z  0.8
2012 Melquiond ASJ, Karaca E, Kastritis PL, Bonvin AMJJ. Next challenges in protein-protein docking: From proteome to interactome and beyond Wiley Interdisciplinary Reviews: Computational Molecular Science. 2: 642-651. DOI: 10.1002/wcms.91  0.8
2012 Schmitz C, Melquiond ASJ, de Vries SJ, Karaca E, van Dijk M, Kastritis PL, Bonvin AMJJ. Protein-Protein Docking with HADDOCK Nmr of Biomolecules: Towards Mechanistic Systems Biology. 520-535. DOI: 10.1002/9783527644506.ch32  0.8
2012 Kastritis PL, Bonvin AMJJ. Predicting and dissecting high-order molecular complexity by information-driven biomolecular docking Antimicrobial Drug Discovery: Emerging Strategies. 232-246.  0.8
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  0.8
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  0.8
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  0.56
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  0.8
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  0.8
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  0.92
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  0.56
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  0.8
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  0.8
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  0.8
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  0.68
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  0.8
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  0.8
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  0.8
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  0.8
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  0.56
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  0.56
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  0.8
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  0.8
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  0.48
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  0.8
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  0.4
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  0.8
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  0.8
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  0.8
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  1
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  0.56
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  0.56
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.56
2008 van Dijk M, Bonvin AM. A protein-DNA docking benchmark. Nucleic Acids Research. 36: e88. PMID 18583363 DOI: 10.1093/nar/gkn386  0.56
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  0.52
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  0.8
2008 De Vries SJ, Van Dijk M, Bonvin AMJJ. The Prediction of Macromolecular Complexes by Docking Prediction of Protein Structures, Functions, and Interactions. 211-230. DOI: 10.1002/9780470741894.ch9  0.56
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  0.8
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  0.72
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  0.8
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  0.8
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  0.72
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  0.68
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  0.8
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  0.72
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  0.8
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  1
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  0.8
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  0.56
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  1
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  1
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  0.8
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  0.8
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  0.72
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  0.8
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  0.8
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  1
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  0.8
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  1
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  1
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  1
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  1
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  0.72
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  0.8
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  0.4
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  1
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  0.8
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  1
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  0.8
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  1
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  0.36
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  1
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  0.4
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  0.8
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  0.8
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  1
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  1
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  0.8
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  0.8
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  0.8
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  1
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  0.8
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.32
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  1
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: 10.1006/jmbi.1995.0173  1
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  1
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  1
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  1
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  1
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  1
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  1
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