Panagiotis L. Kastritis, Ph.D. - Publications

2008-2013 Chemistry Utrecht University, Utrecht, Netherlands 
 2013-2018 Structural and Computational Biology Unit EMBL Heidelberg 
 2018- Biochemistry and Biotechnology Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Sachsen-Anhalt, Germany 
Biochemistry, Biophysics, Biology, Bioinformatics

59 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
2021 Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P. Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum. Plos One. 16: e0254429. PMID 34242379 DOI: 10.1371/journal.pone.0254429  1
2021 Drikos I, Boutou E, Kastritis PL, Vorgias CE. Mutations Alter the Subcellular Localization of BRCA1 . Anticancer Research. 41: 2953-2962. PMID 34083286 DOI: 10.21873/anticanres.15077  0.01
2021 Kyrilis FL, Belapure J, Kastritis PL. Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. Frontiers in Molecular Biosciences. 8: 660542. PMID 33937337 DOI: 10.3389/fmolb.2021.660542  1
2021 Rehkamp A, Tänzler D, Tüting C, Kastritis PL, Iacobucci C, Ihling CH, Kipping M, Koch KW, Sinz A. First 3D-Structural Data of Full-length Guanylyl Cyclase 1 in Rod-Outer-Segment Preparations of Bovine Retina by Cross-linking/Mass Spectrometry. Journal of Molecular Biology. 166947. PMID 33744315 DOI: 10.1016/j.jmb.2021.166947  1
2021 Niemeyer M, Castillo EM, Ihling CH, Iacobucci C, Wilde V, Hellmuth A, Hoehenwarter W, Samodelov SL, Zurbriggen MD, Kastritis PL, Sinz A, Villalobos LIAC. Author Correction: Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies. Nature Communications. 12: 1768. PMID 33723268 DOI: 10.1038/s41467-021-22151-x  1
2021 Kyrilis FL, Semchonok DA, Skalidis I, Tüting C, Hamdi F, O'Reilly FJ, Rappsilber J, Kastritis PL. Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts. Cell Reports. 34: 108727. PMID 33567276 DOI: 10.1016/j.celrep.2021.108727  1
2021 Sorzano COS, Semchonok D, Lin SC, Lo YC, Vilas JL, Jiménez-Moreno A, Gragera M, Vacca S, Maluenda D, Martínez M, Ramírez-Aportela E, Melero R, Cuervo A, Conesa JJ, Conesa P, ... ... Kastritis PL, et al. Algorithmic robustness to preferred orientations in Single Particle Analysis by CryoEM. Journal of Structural Biology. 107695. PMID 33421545 DOI: 10.1016/j.jsb.2020.107695  0.01
2020 Rodrigues JPGLM, Barrera-Vilarmau S, M C Teixeira J, Sorokina M, Seckel E, Kastritis PL, Levitt M. Insights on cross-species transmission of SARS-CoV-2 from structural modeling. Plos Computational Biology. 16: e1008449. PMID 33270653 DOI: 10.1371/journal.pcbi.1008449  1
2020 Sorokina M, M C Teixeira J, Barrera-Vilarmau S, Paschke R, Papasotiriou I, Rodrigues JPGLM, Kastritis PL. Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design. Scientific Data. 7: 309. PMID 32938937 DOI: 10.1038/S41597-020-00652-6  1
2020 Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Förster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM. Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress. Proceedings of the National Academy of Sciences of the United States of America. PMID 32855298 DOI: 10.1073/Pnas.2005301117  1
2020 Skalidis I, Tüting C, Kastritis PL. Unstructured regions of large enzymatic complexes control the availability of metabolites with signaling functions. Cell Communication and Signaling : Ccs. 18: 136. PMID 32843078 DOI: 10.1186/S12964-020-00631-9  1
2020 Tüting C, Iacobucci C, Ihling CH, Kastritis PL, Sinz A. Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity. Scientific Reports. 10: 12618. PMID 32724211 DOI: 10.1038/S41598-020-69313-3  1
2020 Modicano P, Neumann R, Schüller M, Holthof J, Kyrilis FL, Hamdi F, Kastritis PL, Mäder K, Ann Dailey L. Enhanced optical imaging properties of lipid nanocapsules as vehicles for fluorescent conjugated polymers. European Journal of Pharmaceutics and Biopharmaceutics : Official Journal of Arbeitsgemeinschaft Fur Pharmazeutische Verfahrenstechnik E.V. PMID 32707286 DOI: 10.1016/J.Ejpb.2020.07.017  1
2020 Rodrigues JP, Barrera-Vilarmau S, Teixeira JM, Seckel E, Kastritis P, Levitt M. Insights on cross-species transmission of SARS-CoV-2 from structural modeling. Biorxiv : the Preprint Server For Biology. PMID 32577636 DOI: 10.1101/2020.06.05.136861  1
2020 Marušič N, Otrin L, Zhao Z, Lira RB, Kyrilis FL, Hamdi F, Kastritis PL, Vidaković-Koch T, Ivanov I, Sundmacher K, Dimova R. Constructing artificial respiratory chain in polymer compartments: Insights into the interplay between oxidase and the membrane. Proceedings of the National Academy of Sciences of the United States of America. PMID 32554497 DOI: 10.1073/Pnas.1919306117  1
2020 Niemeyer M, Moreno Castillo E, Ihling CH, Iacobucci C, Wilde V, Hellmuth A, Hoehenwarter W, Samodelov SL, Zurbriggen MD, Kastritis PL, Sinz A, Calderón Villalobos LIA. Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies. Nature Communications. 11: 2277. PMID 32385295 DOI: 10.1038/S41467-020-16147-2  1
2020 Hamdi F, Tüting C, Semchonok DA, Visscher KM, Kyrilis FL, Meister A, Skalidis I, Schmidt L, Parthier C, Stubbs MT, Kastritis PL. 2.7 Å cryo-EM structure of vitrified M. musculus H-chain apoferritin from a compact 200 keV cryo-microscope. Plos One. 15: e0232540. PMID 32374767 DOI: 10.1371/Journal.Pone.0232540  1
2019 Kyrilis FL, Meister A, Kastritis PL. Integrative biology of native cell extracts: a new era for structural characterization of life processes. Biological Chemistry. PMID 31091193 DOI: 10.1515/Hsz-2018-0445  1
2019 Hampoelz B, Andres-Pons A, Kastritis P, Beck M. Structure and Assembly of the Nuclear Pore Complex. Annual Review of Biophysics. PMID 30943044 DOI: 10.1146/Annurev-Biophys-052118-115308  1
2018 Kastritis PL, Gavin AC. Enzymatic complexes across scales. Essays in Biochemistry. 62: 501-514. PMID 30315098 DOI: 10.1042/Ebc20180008  0.64
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  1
2017 Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, et al. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Molecular Systems Biology. 13: 936. PMID 28743795 DOI: 10.15252/Msb.20167412  1
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  1
2017 Ichikawa M, Liu D, Kastritis PL, Basu K, Hsu TC, Yang S, Bui KH. Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins. Nature Communications. 8: 15035. PMID 28462916 DOI: 10.1038/Ncomms15035  0.01
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  1
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  1
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  1
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, ... ... Kastritis PL, 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  1
2016 Krüger M, Kalbacher H, Kastritis PL, Bischof J, Barth H, Henne-Bruns D, Vorgias C, Sarno S, Pinna LA, Knippschild U. New potential peptide therapeutics perturbing CK1δ/α-tubulin interaction. Cancer Letters. PMID 26996302 DOI: 10.1016/J.Canlet.2016.03.021  0.01
2016 Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M. Spatiotemporal variation of mammalian protein complex stoichiometries. Genome Biology. 17: 47. PMID 26975353 DOI: 10.1186/S13059-016-0912-5  1
2016 Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW. The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex. Plos One. 11: e0146457. PMID 26745716 DOI: 10.1371/Journal.Pone.0146457  1
2015 von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, et al. In situ structural analysis of the human nuclear pore complex. Nature. 526: 140-3. PMID 26416747 DOI: 10.1038/Nature15381  1
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  1
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  1
2015 Gaik M, Flemming D, von Appen A, Kastritis P, Mücke N, Fischer J, Stelter P, Ori A, Bui KH, Baßler J, Barbar E, Beck M, Hurt E. Structural basis for assembly and function of the Nup82 complex in the nuclear pore scaffold. The Journal of Cell Biology. 208: 283-97. PMID 25646085 DOI: 10.1083/Jcb.201411003  1
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  1
2014 Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, et al. An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. Nucleic Acids Research. 42: 13525-33. PMID 25398899 DOI: 10.1093/Nar/Gku1147  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Kastritis PL, Bonvin AMJJ. Predicting and dissecting high-order molecular complexity by information-driven biomolecular docking Antimicrobial Drug Discovery: Emerging Strategies. 232-246.  1
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, ... ... Kastritis PL, 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  1
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  1
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  1
2011 Kastritis PL, Bonvin AMJJ. Erratum: Are scoring functions in protein - Protein Docking Ready to predict interactomes? Clues from a novel binding affinity benchmark (Journal of Proteome Research (2010) 9 (2216-2225) Journal of Proteome Research. 10: 921-922. DOI: 10.1021/Pr101118T  1
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  1
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  1
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  1
2007 Kastritis PL, Papandreou NC, Hamodrakas SJ. Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs. International Journal of Biological Macromolecules. 41: 447-53. PMID 17675150 DOI: 10.1016/J.Ijbiomac.2007.06.005  1
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