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Mikael Trellet - Publications

Affiliations: 
Utrecht University, Utrecht, Netherlands 
Area:
molecular modeling, protein-peptide, docking
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23 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
2024 Honorato RV, Trellet ME, Jiménez-García B, Schaarschmidt JJ, Giulini M, Reys V, Koukos PI, Rodrigues JPGLM, Karaca E, van Zundert GCP, Roel-Touris J, van Noort CW, Jandová Z, Melquiond ASJ, Bonvin AMJJ. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nature Protocols. PMID 38886530 DOI: 10.1038/s41596-024-01011-0  0.809
2019 Morris C, Andreetto P, Banci L, Bonvin AMJJ, Chojnowski G, Cano LD, Carazo JM, Conesa P, Daenke S, Damaskos G, Giachetti A, Haley NEC, Hekkelman ML, Heuser P, Joosten RP, ... ... Trellet ME, et al. West-Life: A Virtual Research Environment for structural biology. Journal of Structural Biology: X. 1: 100006. PMID 32647812 DOI: 10.1016/j.yjsbx.2019.100006  0.769
2019 Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue LC, Honorato RV, Moreira I, Kurkcuoglu Z, Vangone A, Bonvin AMJJ. An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins. PMID 31886559 DOI: 10.1002/Prot.25869  0.758
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, ... ... Trellet ME, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  0.779
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  0.364
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  0.795
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  0.384
2018 Trellet M, Férey N, Flotyński J, Baaden M, Bourdot P. Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data. Journal of Integrative Bioinformatics. 15. PMID 29982236 DOI: 10.1515/Jib-2018-0004  0.351
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  0.762
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  0.793
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  0.771
2017 Moreira IS, Koukos P, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gumus ZH, Costa J, Bonvin AMJJ. Spoton: A Machine-Learning Approach for Hot-Spot Determination Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.284  0.814
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 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  0.772
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  0.737
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  0.773
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  0.795
2014 Dreher M, Prevoteau-Jonquet J, Trellet M, Piuzzi M, Baaden M, Raffin B, Ferey N, Robert S, Limet S. ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations. Faraday Discussions. 169: 119-42. PMID 25340956 DOI: 10.1039/C3Fd00142C  0.316
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  0.786
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  0.804
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  0.798
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  0.754
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  0.745
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