| Year |
Citation |
Score |
| 2024 |
Kravchenko A, de Vries SJ, Smaïl-Tabbone M, Chauvot de Beauchene I. HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses. Bmc Bioinformatics. 25: 129. PMID 38532339 DOI: 10.1186/s12859-024-05733-6 |
0.303 |
|
| 2021 |
Murail S, de Vries SJ, Rey J, Moroy G, Tufféry P. SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking. Frontiers in Molecular Biosciences. 8: 716466. PMID 34604303 DOI: 10.3389/fmolb.2021.716466 |
0.315 |
|
| 2019 |
Glashagen G, de Vries S, Uciechowska-Kaczmarzyk U, Samsonov SA, Murail S, Tuffery P, Zacharias M. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins. PMID 31785163 DOI: 10.1002/prot.25860 |
0.356 |
|
| 2019 |
Karami Y, Rey J, Postic G, Murail S, Tufféry P, de Vries SJ. DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Research. PMID 31114872 DOI: 10.1093/nar/gkz403 |
0.327 |
|
| 2018 |
Karami Y, Guyon F, De Vries S, Tufféry P. DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. Scientific Reports. 8: 13673. PMID 30209260 DOI: 10.1038/s41598-018-32079-w |
0.331 |
|
| 2017 |
de Vries SJ, Rey J, Schindler CEM, Zacharias M, Tuffery P. The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Research. PMID 28460116 DOI: 10.1093/nar/gkx335 |
0.319 |
|
| 2017 |
Sasse A, de Vries SJ, Schindler CE, de Beauchêne IC, Zacharias M. Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking. Plos One. 12: e0170625. PMID 28118389 DOI: 10.1371/journal.pone.0170625 |
0.304 |
|
| 2016 |
Schindler CE, Chauvot de Beauchêne I, de Vries S, Zacharias M. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins. PMID 27785830 DOI: 10.1002/prot.25196 |
0.33 |
|
| 2016 |
Schindler CE, de Vries SJ, Sasse A, Zacharias M. SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. Structure (London, England : 1993). PMID 27427479 DOI: 10.1016/j.str.2016.06.007 |
0.364 |
|
| 2016 |
de Vries SJ, Chauvot de Beauchêne I, Schindler CE, Zacharias M. Cryo-EM Data Is Superior to Contact and Interface Information in Integrative Modeling. Biophysical Journal. PMID 26846888 DOI: 10.1016/j.bpj.2015.12.038 |
0.412 |
|
| 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 |
0.69 |
|
| 2015 |
de Vries SJ, Schindler CE, Chauvot de Beauchêne I, Zacharias M. A web interface for easy flexible protein-protein docking with ATTRACT. Biophysical Journal. 108: 462-5. PMID 25650913 DOI: 10.1016/j.bpj.2014.12.015 |
0.337 |
|
| 2015 |
Schindler CE, de Vries SJ, Zacharias M. iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement. Proteins. 83: 248-58. PMID 25402278 DOI: 10.1002/prot.24728 |
0.406 |
|
| 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 |
0.704 |
|
| 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 |
0.699 |
|
| 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 |
0.602 |
|
| 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 |
0.751 |
|
| 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 |
0.663 |
|
| 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 |
0.768 |
|
| 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 |
0.65 |
|
| 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 |
0.785 |
|
| 2010 |
Koenderink JJ, Albertazzi L, van Doorn AJ, van Ee R, van de Grind WA, Kappers AM, Lappin JS, Norman JF, Stijn Oomes AH, te Pas SP, Phillips F, Pont SC, Richards WA, Todd JT, Verstraten FA, ... de Vries S, et al. Does monocular visual space contain planes? Acta Psychologica. 134: 40-7. PMID 20053390 DOI: 10.1016/j.actpsy.2009.12.002 |
0.728 |
|
| 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 |
0.603 |
|
| 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 |
0.534 |
|
| 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 |
0.617 |
|
| 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 |
0.765 |
|
| 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 |
0.576 |
|
| 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 |
0.65 |
|
| 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 |
0.791 |
|
| 1995 |
de Vries SC, Werkhoven P. Cross-modal slant and curvature matching of stereo- and motion-induced surfaces. Perception & Psychophysics. 57: 1175-86. PMID 8539092 DOI: 10.3758/BF03208373 |
0.581 |
|
| 1994 |
de Vries SC, Kappers AM, Koenderink JJ. Influence of surface attitude and curvature scaling on discrimination of binocularly presented curved surfaces. Vision Research. 34: 2409-23. PMID 7975280 DOI: 10.1016/0042-6989(94)90285-2 |
0.4 |
|
| 1993 |
de Vries SC, Kappers AM, Koenderink JJ. Shape from stereo: a systematic approach using quadratic surfaces. Perception & Psychophysics. 53: 71-80. PMID 8433907 DOI: 10.3758/BF03211716 |
0.359 |
|
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