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Mikael Trellet - Publications

Affiliations: 
Utrecht University, Utrecht, Netherlands 
Area:
molecular modeling, protein-peptide, docking
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22/29 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 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  0.766
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  0.752
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  0.775
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  0.367
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  0.792
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  0.374
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  0.341
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  0.759
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  0.79
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  0.77
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  0.812
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  0.789
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  0.77
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  0.733
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  0.766
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  0.794
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  0.309
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  0.783
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  0.797
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  0.751
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  0.743
Low-probability matches (unlikely to be authored by this person)
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, ... ... Trellet M, et al. Sharing Data from Molecular Simulations. Journal of Chemical Information and Modeling. PMID 31525920 DOI: 10.1021/Acs.Jcim.9B00665  0.279
2020 Trellet M, van Zundert G, Bonvin AMJJ. Protein-Protein Modeling Using Cryo-EM Restraints. Methods in Molecular Biology (Clifton, N.J.). 2112: 145-162. PMID 32006284 DOI: 10.1007/978-1-0716-0270-6_11  0.262
2020 Jiménez-García B, Teixeira JMC, Trellet M, Rodrigues JPGLM, Bonvin AMJJ. PDB-tools web: A user-friendly interface for the manipulation of PDB files. Proteins. PMID 33111403 DOI: 10.1002/prot.26018  0.238
2011 Chamot-Rooke J, Mikaty G, Malosse C, Soyer M, Dumont A, Gault J, Imhaus AF, Martin P, Trellet M, Clary G, Chafey P, Camoin L, Nilges M, Nassif X, Duménil G. Posttranslational modification of pili upon cell contact triggers N. meningitidis dissemination. Science (New York, N.Y.). 331: 778-82. PMID 21311024 DOI: 10.1126/Science.1200729  0.211
2014 Trellet M, Ferey N, Baaden M, Bourdot P. Content-guided navigation in multimeric molecular complexes Bioimaging 2014 - 1st International Conference On Bioimaging, Proceedings; Part of 7th International Joint Conference On Biomedical Engineering Systems and Technologies, Biostec 2014. 76-81.  0.157
2015 Trellet M, Ferey N, Baaden M, Bourdot P. Content and task based navigation for structural biology in 3D environments 2015 Ieee 1st International Workshop On Virtual and Augmented Reality For Molecular Science, Varms@Ieeevr 2015. 31-36. DOI: 10.1109/VARMS.2015.7151726  0.119
2020 Rabouw HH, Visser LJ, Passchier TC, Langereis MA, Liu F, Giansanti P, van Vliet ALW, Dekker JG, van der Grein SG, Saucedo JG, Anand AA, Trellet ME, Bonvin AMJJ, Walter P, Heck AJR, et al. Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association. Nature Microbiology. PMID 32690955 DOI: 10.1038/S41564-020-0759-0  0.1
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