Κρυογονική ηλεκτρονική μικροσκοπία (Cryo-EM)

• Zamanos A, Koromilas P, Bouritsas G, Kastritis PL, Panagakis Y. Self-supervised learning for generalizable particle picking in cryo-EM micrographs. Cell Rep Methods. 2025 Jul 21;5(7):101089.
  doi: 10.1016/j.crmeth.2025.101089. Epub 2025 Jul 7.
• Winter A, Lange J, Hamdi F, Kastritis PL, Haase F. Evidence of heteroepitaxy and solid solutions in lattice matched ternary covalent organic framework systems. J Am Chem Soc. 2025 Jun 11;147(23):19702–19710.
  doi: 10.1021/jacs.5c02502. Epub 2025 Jun 2.
• Hamdi F, Skalidis I, Schwerin IK, Belapure J, Semchonok DA, Kyrilis FL, Tüting C, Müller J, Künze G, Kastritis PL. Direct evidence of acid-driven protein desolvation. bioRxiv. Preprint posted 2025 Sep 1.
  doi: 10.1101/2025.09.01.673474

• Träger T, Kastritis PL. Cracking the code of cellular protein-protein interactions: Alphafold and whole-cell crosslinking to the rescue. Mol Syst Biol. 2024 Apr 12;19(4):e11587.
  doi: 10.15252/msb.202311587
• Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, et al. Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol. 2024 May 10;7(1):557.
  doi: 10.1038/s42003-024-06204-7
• Skalidis I, Kyrilis FL, Tüting C, Hamdi F, Träger TK, et al. Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon. Commun Biol. 2024 May 22;6(1):552.
  doi: 10.1038/s42003-023-04885-0
• Winter A, Hamdi F, Eichhöfer A, Saalwächter K, Kastritis PL, Haase F. Enhancing structural control in covalent organic frameworks through steric interaction-driven linker design. Chem Sci. 2024 Aug 13;15(35):14449–14457.
  doi: 10.1039/d4sc03461a
• Träger TK, Kyrilis FL, Hamdi F, Tüting C, Alfes M, Hofmann T, Schmidt C, Kastritis PL. Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway. Proc Natl Acad Sci U S A. 2024 Aug 20;121(34):e2400912121.
  doi: 10.1073/pnas.2400912121
• Opatíková M, Semchonok DA, Kopečný D, Ilík P, Pospíšil P, Ilíková I, et al. Cryo-EM structure of a plant photosystem II supercomplex with light harvesting protein Lhcb8 and α-tocopherol. Nat Plants. 2024 Aug;9(8):1359–1369.
  doi: 10.1038/s41477-023-01483-0
• Träger TK, Tüting C, Kastritis PL. The human touch: Utilizing AlphaFold 3 to analyze structures of endogenous metabolons. Structure. 2024 Oct 3;32(10):1555–1562.
  doi: 10.1016/j.str.2024.08.018
• Kyrilis FL, Low JKK, Mackay JP, Kastritis PL. Structural biology in cellulo: Minding the gap between conceptualization and realization. Curr Opin Struct Biol. 2024 Aug;87:102843. doi: 10.1016/j.sbi.2024.102843. Epub 2024 May 23.
• Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL. Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol. 2024 May 10;7(1):557. doi: 10.1038/s42003-024-06204-7. SJR: 5.9. Citations: 3.
• Otrin N, Otrin L, Bednarz C, Träger TK, Hamdi F, Kastritis PL, Ivanov I, Sundmacher K.
  Protein-Rich Rafts in Hybrid Polymer/Lipid Giant Unilamellar Vesicles. Biomacromolecules. 2024 Feb 12;25(2):778-791. doi: 10.1021/acs.biomac.3c00972. SJR: 6.2. Citations: 0.
• Schmitt FJ, Mehmood AS, Tüting C, Phan HT, Reisdorf J, Rieder F, Ghane Golmohamadi F, Verma R, Kastritis PL, Laufer J. Effect of Molecular Dynamics and Internal Water Contact on the Photophysical Properties of Red pH-Sensitive Proteins. Biochemistry. 2024 Jan 2;63(1):82-93. doi: 10.1021/acs.biochem.3c00444. SJR: 2.9. Citations: 0.

• Semchonok DA, Kyrilis FL, Hamdi F, Kastritis PL*. Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote. J Struct Biol X. 2023 Aug 9;8:100094.
  doi: 10.1016/j.yjsbx.2023.100094. SJR: 3.0. Citations: 0.
• Hassan AH, Ihling C, Iacobucci C, Kastritis PL, Sinz A, Kruse T. The structural principles underlying molybdenum insertase complex assembly. Protein Sci. 2023 Sep;32(9):e4753.
  doi: 10.1002/pro.4753. SJR: 8.0. Citations: 1.
• Tüting C, Schmidt L, Skalidis I, Sinz A, Kastritis PL*. Enabling cryo-EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures. Proteomics. 2023 Sep;23(17):e2200096.
  doi: 10.1002/pmic.202200096. SJR: 3.4. Citations: 2.
• Opatíková M, Semchonok DA, Kopečný D, Ilík P, Pospíšil P, Ilíková I, Roudnický P, Zeljković SĆ, Tarkowski P, Kyrilis FL, Hamdi F, Kastritis PL, Kouřil R. Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and α-tocopherol. Nat Plants. 2023 Aug;9(8):1359-1369.
  doi: 10.1038/s41477-023-01483-0. SJR: 18.0. Citations: 4.
• Zahn T, Zhu Z, Ritoff N, Krapf J, Junker A, Altmann T, Schmutzer T, Tüting C, Kastritis PL, Babben S, Quint M, Pillen K, Maurer A. Novel exotic alleles of EARLY FLOWERING 3 determine plant development in barley. J Exp Bot. 2023 Jun 27;74(12):3630-3650.
  doi: 10.1093/jxb/erad127. SJR: 6.9. Citations: 6.
• Zhou Y, Syed JH, Semchonok DA, Wright E, Kyrilis FL, Hamdi F, Kastritis PL, Bruce BD, Reynolds TB. Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans. J Biol Chem. 2023 Jun;299(6):104756.
  doi: 10.1016/j.jbc.2023.104756. SJR: 4.8. Citations: 1.
• Di Ianni A, Tüting C, Kipping M, Ihling CH, Köppen J, Iacobucci C, Arlt C, Kastritis PL*, Sinz A. Structural assessment of the full-length wild-type tumor suppressor protein p53 by mass spectrometry-guided computational modeling. Sci Rep. 2023 May 25;13(1):8497.
  doi: 10.1038/s41598-023-35437-5. SJR: 4.6. Citations: 3.
• Skalidis I, Kyrilis FL, Tüting C, Hamdi F, Träger TK, Belapure J, Hause G, Fratini M, O’Reilly FJ, Heilmann I, Rappsilber J, Kastritis PL*. Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon. Commun Biol. 2023 May 22;6(1):552.
  doi: 10.1038/s42003-023-04885-0. SJR: 5.9. Citations: 2.
• Träger T, Kastritis PL*. Cracking the code of cellular protein-protein interactions: Alphafold and whole-cell crosslinking to the rescue. Mol Syst Biol. 2023 Apr 12;19(4):e11587.
  doi: 10.15252/msb.202311587. SJR: 9.9. Citations: 2.
• Demisli S, Galani E, Goulielmaki M, Kyrilis FL, Ilić T, Hamdi F, Crevar M, Kastritis PL, Pletsa V, Nallet F, Savić S, Xenakis A, Papadimitriou V. Encapsulation of cannabidiol in oil-in-water nanoemulsions and nanoemulsion-filled hydrogels: A structure and biological assessment study. J Colloid Interface Sci. 2023 Mar 15;634:300-313.
  doi: 10.1016/j.jcis.2022.12.036. SJR: 9.9. Citations: 13.
• Belapure J, Sorokina M, Kastritis PL*. IRAA: A statistical tool for investigating a protein-protein interaction interface from multiple structures. Protein Sci. 2023 Jan;32(1):e4523.
  doi: 10.1002/pro.4523. SJR: 8.0. Citations: 0.

• Janson K, Kyrilis FL, Tüting C, Alfes M, Das M, Träger TK, Schmidt C, Hamdi F, Vargas C, Keller S, Meister A*, Kastritis PL*. Cryo-Electron Microscopy Snapshots of Eukaryotic Membrane Proteins in Native Lipid-Bilayer Nanodiscs. Biomacromolecules. 2022 Dec 12;23(12):5084-5094.
  doi: 10.1021/acs.biomac.2c00935. SJR: 6.2. Citations: 5.
• Tafur L, Hinterndorfer K, Gabus C, Lamanna C, Bergmann A, Sadian Y, Hamdi F, Kyrilis FL, Kastritis PL, Loewith R. Cryo-EM structure of the SEA complex. Nature. 2022 Nov;611(7935):399-404.
  doi: 10.1038/s41586-022-05370-0. SJR: 64.8. Citations: 15.
• Kastritis PL*. An integrative approach to probing transient protein structures in cell extracts. Genetic Engineering & Biotechnology News. 2022 Sep;42(9):68-70.
  doi: 10.1089/gen.42.09.22. SJR: n/a. Citations: 0.
• Wurl A, Ott M, Plato E, Meister A, Hamdi F, Kastritis PL, Blume A, Ferreira TM. Filling the Gap with Long n-Alkanes: Incorporation of C20 and C30 into Phospholipid Membranes. Langmuir. 2022 Jul 19;38(28):8595-8606.
  doi: 10.1021/acs.langmuir.2c00872. SJR: 3.9. Citations: 3.
• Sorokina M, Belapure J, Tüting C, Paschke R, Papasotiriou I, Rodrigues JPGLM, Kastritis PL*. An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation. J Mol Biol. 2022 Jul 15;434(13):167637.
  doi: 10.1016/j.jmb.2022.167637. SJR: 5.6. Citations: 2.
• Marušič N, Otrin L, Rauchhaus J, Zhao Z, Kyrilis FL, Hamdi F, Kastritis PL, Dimova R, Ivanov I, Sundmacher K. Increased efficiency of charge-mediated fusion in polymer/lipid hybrid membranes. Proc Natl Acad Sci U S A. 2022 May 17;119(20):e2122468119.
  doi: 10.1073/pnas.2122468119. SJR: 11.1. Citations: 19.
• Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev. 2022 Apr 27;122(8):7500-7531.
  doi: 10.1021/acs.chemrev.1c00786. SJR: 62.1. Citations: 125.
• Skalidis I, Kyrilis FL, Tüting C, Hamdi F, Chojnowski G, Kastritis PL*. Cryo-EM and artificial intelligence visualize endogenous protein community members. Structure. 2022 Apr 7;30(4):575-589.e6.
  doi: 10.1016/j.str.2022.01.001. SJR: 5.7. Citations: 28.
• Li F, Harvey RD, Modicano P, Hamdi F, Kyrilis F, Müller S, Gruhle K, Kastritis PL, Drescher S, Dailey LA. Investigating bolalipids as solubilizing agents for poorly soluble drugs: Effects of alkyl chain length on solubilization and cytotoxicity. Colloids Surf B Biointerfaces. 2022 Apr;212:112369.
  doi: 10.1016/j.colsurfb.2022.112369. SJR: 5.8. Citations: 4.

• Semchonok DA, Mondal J, Cooper CJ, Schlum K, Li M, Amin M, Sorzano COS, Ramírez-Aportela E, Kastritis PL, Boekema EJ, Guskov A, Bruce BD. Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium. Plant Commun. 2021 Oct 13;3(1):100248.
  doi: 10.1016/j.xplc.2021.100248. SJR: 10.5. Citations: 12.
• Tüting C, Kyrilis FL, Müller J, Sorokina M, Skalidis I, Hamdi F, Sadian Y, Kastritis PL*. Cryo-EM snapshots of a native lysate provide structural insights into a metabolon-embedded transacetylase reaction. Nat Commun. 2021 Nov 26;12(1):6933.
  doi: 10.1038/s41467-021-27287-4. SJR: 16.6. Citations: 28.
• Janson K, Zierath J, Kyrilis FL, Semchonok DA, Hamdi F, Skalidis I, Kopf AH, Das M, Kolar C, Rasche M, Vargas C, Keller S, Kastritis PL*, Meister A*. Solubilization of artificial mitochondrial membranes by amphiphilic copolymers of different charge. Biochim Biophys Acta Biomembr. 2021 Aug 10;1863(12):183725.
  doi: 10.1016/j.bbamem.2021.183725. SJR: 3.4. Citations: 11.
• Otrin L, Witkowska A, Marušič N, Zhao Z, Lira RB, Kyrilis FL, Hamdi F, Ivanov I, Lipowsky R, Kastritis PL, Dimova R, Sundmacher K, Jahn R, Vidaković-Koch T. En route to dynamic life processes by SNARE-mediated fusion of polymer and hybrid membranes. Nat Commun. 2021 Aug 17;12(1):4972.
  doi: 10.1038/s41467-021-25294-z. SJR: 16.6. Citations: 24.
• 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. 2021 Jul 9;16(7):e0254429.
  doi: 10.1371/journal.pone.0254429. SJR: 3.7. Citations: 8.
• Drikos I, Boutou E, Kastritis PL, Vorgias CE. BRCA1-BRCT mutations alter the subcellular localization of BRCA1 in vitro. Anticancer Res. 2021 Jun;41(6):2953-2962.
  doi: 10.21873/anticanres.15077. SJR: 2.0. Citations: 5.
• Hoffmann M, Haselberger D, Hofmann T, Müller L, Janson K, Meister A, Das M, Vargas C, Keller S, Kastritis PL, Schmidt C, Hinderberger D. Nanoscale Model System for the Human Myelin Sheath. Biomacromolecules. 2021 Sep 13;22(9):3901-3912.
  doi: 10.1021/acs.biomac.1c00714. SJR: 6.2. Citations: 6.
• 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. J Mol Biol. 2021 May 14;433(10):166947.
  doi: 10.1016/j.jmb.2021.166947. SJR: 5.6. Citations: 7.
• Kyrilis FL, Belapure J, Kastritis PL*. Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist’s Perspective. Front Mol Biosci. 2021 Apr 15;8:660542.
  doi: 10.3389/fmolb.2021.660542. SJR: 5.0. Citations: 12.
• 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 Rep. 2021 Feb 9;34(6):108727.
  doi: 10.1016/j.celrep.2021.108727. SJR: 8.8. Citations: 41.
• Hofmann T, Barth M, Meister A, Kastritis PL, Schmidt C. Thin‐Layer chromatography and coomassie staining of phospholipids for fast and simple lipidomics sample preparation.
  Anal. Sens. 2021 accepted author manuscript.
  doi: 10.1002/anse.202100029. SJR: n/a. Citations: 5.
• 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, Losana P, Caño LD, de la Morena JJ, Fonseca YC, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro F, Herreros D, Kastritis PL, Marabini R, Bruce BD, Carazo JM. Algorithmic robustness to preferred orientations in single particle analysis by CryoEM. J Struct Biol. 2021 Mar;213(1):107695.
  doi: 10.1016/j.jsb.2020.107695. SJR: 3.0. Citations: 20.

• 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 Comput Biol. 2020 Dec 3;16(12):e1008449.
  doi: 10.1371/journal.pcbi.1008449. SJR: 4.3. Citations: 64.
• Skalidis I, Tüting C, Kastritis PL*. Unstructured regions of large enzymatic complexes control the availability of metabolites with signaling functions. Cell Commun Signal. 2020 Aug 26;18(1):136.
  doi: 10.1186/s12964-020-00631-9. SJR: 8.4. Citations: 15.
• 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. Sci Data. 2020 Sep 16;7(1):309.
  doi: 10.1038/s41597-020-00652-6. SJR: 9.8. Citations: 25.
• 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. Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22157-22166.
  doi: 10.1073/pnas.2005301117. SJR: 11.1. Citations: 27.
• Modicano P, Neumann PR, 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. Eur J Pharm Biopharm. 2020 Sep;154:297-308.
  doi: 10.1016/j.ejpb.2020.07.017. SJR: 4.9. Citations: 10.
• Tüting C#, Iacobucci C#, Ihling CH, Kastritis PL*, Sinz A*. Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity. Sci Rep. 2020 Jul 28;10(1):12618.
  doi: 10.1038/s41598-020-69313-3. SJR: 4.6. Citations: 31.
• 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 bo 3 oxidase and the membrane. Proc Natl Acad Sci U S A. 2020 Jun 30;117(26):15006-15017.
  doi: 10.1073/pnas.1919306117. SJR: 11.1. Citations: 47.
• 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. Nat Commun. 2020 May 8;11(1):2277.
  doi: 10.1038/s41467-020-16147-2. SJR: 16.6. Citations: 38.

• Kyrilis FL, Meister A, Kastritis PL*. Integrative biology of native cell extracts: a new era for structural characterization of life processes. Biol Chem. 2019 Jun 26;400(7):831-846.
  doi: 10.1515/hsz-2018-0445. SJR: 3.7. Citations: 27.
• Hampoelz B, Andres-Pons A, Kastritis PL, Beck M. Structure and Assembly of the Nuclear Pore Complex. Annu Rev Biophys. 2019 May 6;48:515-536.
  doi: 10.1146/annurev-biophys-052118-115308. SJR: 12.4. Citations: 209.
• 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. 2020 May 6;15(5):e0232540.
  doi: 10.1371/journal.pone.0232540. SJR: 3.7. Citations: 18.

• Kastritis PL#, Gavin AC. Enzymatic complexes across scales. Essays Biochem. 2018 Oct 26;62(4):501-514.
  doi: 10.1042/EBC20180008. SJR: 6.4. Citations: 44.
• Bonvin AMJJ, Karaca E, Kastritis PL, Rodrigues JPGLM. Defining distance restraints in HADDOCK. Nat Protoc. 2018 Jul;13(7):1503.
  doi: 10.1038/s41596-018-0017-6. SJR: 14.8. Citations: 21.

• 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, Beck M, Gavin AC. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol Syst Biol. 2017 Jul 25;13(7):936.
  doi: 10.15252/msb.20167412. SJR: 9.9. Citations: 111.
• 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. Nat Commun. 2017 May 2;8:15035.
  doi: 10.1038/ncomms15035. SJR: 16.6. Citations: 108.
• 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 round 1. Proteins. 2017 Mar;85(3):417-423.
  doi: 10.1002/prot.25198. SJR: 2.9. Citations: 54.

• Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics. 2016 Dec 1;32(23):3676-3678.
  d doi: 10.1093/bioinformatics/btw514. SJR: 5.8. Citations: 887.
• Ori A, Iskar M, Buczak K, Kastritis PL, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M. Spatiotemporal variation of mammalian protein complex stoichiometries. Genome Biol. 2016 Mar 14;17:47.
  doi: 10.1186/s13059-016-0912-5. SJR: 12.3. Citations: 105.
• 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, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. 2016 Sep;84 Suppl 1(Suppl Suppl 1):323-48.
  oi: 10.1002/prot.25007. SJR: 2.9. Citations: 164.
• 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. Front Mol Biosci. 2016 Aug 31;3:46.
  doi: 10.3389/fmolb.2016.00046. SJR: 5.0. Citations: 69.
• 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 Lett. 2016 Jun 1;375(2):375-383.
  doi: 10.1016/j.canlet.2016.03.021. SJR: 9.7. Citations: 13.
• van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol. 2016 Feb 22;428(4):720-725.
  doi: 10.1016/j.jmb.2015.09.014. SJR: 5.6. Citations: 2314.
• Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis PL, 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. 2016 Jan 8;11(1):e0146457.
  doi: 10.1371/journal.pone.0146457. SJR: 3.7. Citations: 20.

2015

• von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis PL, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M. In situ structural analysis of the human nuclear pore complex. Nature. 2015 Oct 1;526(7571):140-143.
  doi: 10.1038/nature15381. SJR: 64.8. Citations: 396.
• 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. J Mol Biol. 2015 Sep 25;427(19):3031-41.
  doi: 10.1016/j.jmb.2015.07.016. SJR: 5.6. Citations: 422.
• Visscher KM#, Kastritis PL#, Bonvin AM. Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins. 2015 Mar;83(3):445-58.
  doi: 10.1002/prot.24741. SJR: 2.9. Citations: 25.
• Gaik M, Flemming D, von Appen A, Kastritis PL, 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. J Cell Biol. 2015 Feb 2;208(3):283-97.
  doi: 10.1083/jcb.201411003. SJR: 7.8. Citations: 69.

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, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P. An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. Nucleic Acids Res. 2014 Dec 16;42(22):13525-33.
  doi: 10.1093/nar/gku1147. SJR: 14.9. Citations: 65.
• 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. J Mol Biol. 2014 Jul 15;426(14):2632-52.
  doi: 10.1016/j.jmb.2014.04.017. SJR: 5.6. Citations: 128.
• 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, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI. Proteins. 2014 Apr;82(4):620-32.
  doi: 10.1002/prot.24439. SJR: 2.9. Citations: 61.
• Kastritis PL#, Rodrigues JP, Bonvin AM. HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. J Chem Inf Model. 2014 Mar 24;54(3):826-36.
  doi: 10.1021/ci4005332. SJR: 5.6. Citations: 37.

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. 2013 Dec;81(12):2119-28.
  doi: 10.1002/prot.24382. SJR: 2.9. Citations: 75.
• Kastritis PL#, Bonvin AM. Molecular origins of binding affinity: seeking the Archimedean point. Curr Opin Struct Biol. 2013 Dec;23(6):868-77.
  doi: 10.1016/j.sbi.2013.07.001. SJR: 6.8. Citations: 47.
• 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, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 2013 Nov;81(11):1980-7.
  doi: 10.1002/prot.24356. SJR: 2.9. Citations: 111.
• van Dijk M, Visscher KM, Kastritis PL, Bonvin AM. Solvated protein-DNA docking using HADDOCK. J Biomol NMR. 2013 May;56(1):51-63.
  doi: 10.1007/s10858-013-9734-x. SJR: 2.7. Citations: 24.
• Kastritis PL#, Visscher KM, van Dijk AD, Bonvin AM. Solvated protein-protein docking using Kyte-Doolittle-based water preferences. Proteins. 2013 Mar;81(3):510-8.
  doi: 10.1002/prot.24210. SJR: 2.9. Citations: 34.
• Kastritis PL#, Bonvin AM. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface. 2012 Dec 12;10(79):20120835.
  doi: 10.1098/rsif.2012.0835. SJR: 3.9. Citations: 537.

• Bonvin AMJJ, van Dijk M, Karaca E, Kastritis PL, Melquiond ASJ, Schmitz C, de Vries SJ
  HADDOCK.  Encyclopedia of Biophysics, 2013 pp. 943.
  doi: 10.1007/978-3-642-16712-6. SJR: n/a. Citations: 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, 2012 pp. 520 – 535.
  doi: 10.1002/9783527644506.ch32. SJR: n/a. Citations: 9.

• Kastritis PL#, Bonvin AM. Predicting and dissecting high-order molecular complexity by information-driven biomolecular docking. Antimicrobial drug discovery: emerging strategies, 2012 pp. 232-246.
  doi: 10.1079/9781845939434.0232. SJR: n/a. Citations: 2.
• Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, Bonvin AM. Clustering biomolecular complexes by residue contacts similarity. Proteins. 2012 Jul;80(7):1810-7.
  doi: 10.1002/prot.24078. SJR: 2.9. Citations: 117.

• • Kastritis PL#, van Dijk AD, Bonvin AM. Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach. Methods Mol Biol. 2012;819:355-74.
    doi: 10.1007/978-1-61779-465-0_22. SJR: n/a. Citations: 25.
• Melquiond ASJ, Karaca E, Kastritis PL, Bonvin AMJJ. Next challenges in protein–protein docking: from proteome to interactome and beyond. WIRES Comp Mol Sci. 2012 ;(2):642-651.
  doi: 10.1002/wcms.91. SJR: 11.4. Citations: 33.

2011

• Fleishman SJ, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011 Nov 25;414(2):289-302.
  doi: 10.1016/j.jmb.2011.09.031. SJR: 5.6. Citations: 156.
• 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. 2011 Apr 4;6(4):e18127.
  doi: 10.1371/journal.pone.0018127. SJR: 3.7. Citations: 204.
• Kastritis PL#, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J. A structure-based benchmark for protein-protein binding affinity. Protein Sci. 2011 Mar;20(3):482-91.
  doi: 10.1002/pro.580. Epub 2011 Feb 16. SJR: 8.0. Citations: 327.

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. 2010 Nov 15;78(15):3242-9.
  doi: 10.1002/prot.22814. SJR: 2.9. Citations: 53.
• Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Mol Cell Proteomics. 2010 Aug;9(8):1784-94.
  doi: 10.1074/mcp.M000051-MCP201. SJR: 7.0. Citations: 154.
• Kastritis PL#, Bonvin AM. Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J Proteome Res. 2010 May 7;9(5):2216-25.
  doi: 10.1021/pr9009854. SJR: 4.4. Citations: 285.

2007

• Kastritis PL#, Papandreou NC, Hamodrakas SJ. Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs. Int J Biol Macromol. 2007 Oct 1;41(4):447-53.
  doi: 10.1016/j.ijbiomac.2007.06.005. SJR: 8.2. Citations: 81.

On the binding affinity of macromolecular complexes: daring to ask why proteins interact. (in English, abstract in Greek)
Kastritis PL. Utrecht University, Department of Chemistry, Ph.D. Thesis 2012 pp. 1-343 (in English)
Ph.D. Thesis. 2012.

Biophysical studies on the inhibition of the enzyme dihydrofolate reductase by novel inhibitors and its structural adaptation in extreme environments. (Βιοφυσικές μελέτες στην αναστολή του ενζύμου διυδροφολική αναγωγάση (DHFR) από πρότυπους αναστολείς και στην δομική προσαρμοφή του σε ακραίες συνθήκες) (in Greek, abstract in English)
Kastritis PL. National and Kapodistrian University of Athens, Department of Biology, Diploma Thesis 2007 pp.1-134 (in Greek)
Diploma Thesis. 2007.

• 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, Beck M, Gavin AC. Capturing protein communities by structural proteomics in a
  thermophilic eukaryote. Mol Syst Biol. 2017 Jul 25;13(7):936.
  doi: 10.15252/msb.20167412. SJR: 9.9. Citations: 111.
• Sorokina M, Belapure J, Tüting C, Paschke R, Papasotiriou I, Rodrigues JPGLM, Kastritis PL*. An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation. J Mol Biol. 2022 Jul 15;434(13):167637.
  doi: 10.1016/j.jmb.2022.167637.
• Kyrilis FL, Meister A, Kastritis PL*. Integrative biology of native cell extracts: a new
  era for structural characterization of life processes. Biol Chem. 2019 Jun 26;400(7):831-846.
  doi: 10.1515/hsz-2018-0445. SJR: 3.7. Citations: 27.

• Bonvin AMJJ, van Dijk M, Karaca E, Kastritis PL, Melquiond ASJ, Schmitz C, de Vries SJ
  HADDOCK.  Encyclopedia of Biophysics, 2013 pp. 943.
  doi: 10.1007/978-3-642-16712-6. SJR: n/a. Citations: 1.

• 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, 2012 pp. 520 – 535.
  doi: 10.1002/9783527644506.ch32. SJR: n/a. Citations: 9.

• • Kastritis PL#, Bonvin AM. Predicting and dissecting high-order molecular complexity by information-driven biomolecular docking. Antimicrobial drug discovery: emerging strategies, 2012 pp. 232-246.
    doi: 10.1079/9781845939434.0232. SJR: n/a. Citations: 2.

• • Kastritis PL#, van Dijk AD, Bonvin AM. Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach. Methods Mol Biol. 2012;819:355-74.
    doi: 10.1007/978-1-61779-465-0_22. SJR: n/a. Citations: 25.

2022

• Zahn, T.;  Zhu, Z.;  Ritoff, N.;  Krapf, J.;  Junker, A.;  Altmann, T.;  Schmutzer, T.;  Tüting, C.;  Kastritis, P. L.;  Babben, S.;  Quint, M.;  Pillen, K.; Maurer, A., Exotic alleles of EARLY FLOWERING 3 determine plant development and grain yield in barley. bioRxiv 2022, 2022.07.15.500212.
• Semchonok, D. A.;  Siponen, M. I.;  Tüting, C.;  Charras, Q.;  Kyrilis, F. L.;  Hamdi, F.;  Sadian, Y.;  Jungas, C.; Kastritis, P. L., Cryo-EM structure of the Rhodobaca bogoriensis RC-LH1-PufX dimeric complex at 2.9 Å. bioRxiv 2022, 2022.02.25.481955.
• Schmidt, L.;  Tüting, C.;  Kyrilis, F. L.;  Hamdi, F.;  Semchonok, D. A.;  Hause, G.;  Meister, A.;  Ihling, C.;  Shah, P. N. M.;  Stubbs, M. T.;  Sinz, A.;  Stuart, D. I.; Kastritis, P. L., Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. bioRxiv 2022, 2022.07.15.498668.
• Heinz, V.;  Güler, G.;  Leone, V.;  Madej, M. G.;  Maksimov, S.;  Gärtner, R. M.;  Rudi, O.;  Hamdi, F.;  Kastritis, P. L.;  Mäntele, W.;  Krämer, R.;  Forrest, L. R.;  Perez, C.; Ziegler, C., Osmotic stress response in BetP: How lipids and K+ team up to overcome downregulation. bioRxiv 2022, 2022.06.02.493408.

2020

• Tüting, C.;  Iacobucci, C.;  Ihling, C. H.;  Kastritis, P. L.*; Sinz, A.*, Structural Analysis of 70S Ribosomes by Cross-Linking/Mass Spectrometry Reveals Conformational Plasticity. bioRxiv 2020, 2020.05.04.077503. [Published in Sci Rep, publication #45]
• Rodrigues, J. P.;  Barrera-Vilarmau, S.;  Teixeira, J. M. C.;  Seckel, E.;  Kastritis, P.L.; Levitt, M., Insights on cross-species transmission of SARS-CoV-2 from structural modeling. bioRxiv 2020, 2020.06.05.136861. [Published in PLOS Comp Biol, publication #50]
• Rehkamp, A.;  Tänzler, D.;  Tüting, C.;  Kastritis, P. L.;  Iacobucci, C.;  Ihling, C. H.;  Kipping, M.;  Koch, K.-W.; Sinz, A., First 3D-Structural Data of Full-length Rod-Outer-Segment Guanylyl Cyclase 1 in Bovine Retina by Cross-linking/Mass Spectrometry. bioRxiv 2020, 2020.09.25.312835. [Published in J Mol Biol, publication #55]

2019

• Niemeyer, M.;  Castillo, E. M.;  Ihling, C. H.;  Iacobucci, C.;  Wilde, V.;  Hellmuth, A.;  Hoehenwarter, W.;  Samodelov, S. L.;  Zurbriggen, M. D.;  Kastritis, P. L.;  Sinz, A.; Calderón Villalobos, L. I. A., Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies. bioRxiv 2019, 787770. [Published in Nature Comm, publication #43]
• Hamdi, F.;  Tüting, C.;  Semchonok, D. A.;  Visscher, K. M.;  Kyrilis, F. L.;  Meister, A.;  Skalidis, I.;  Schmidt, L.;  Parthier, C.;  Stubbs, M. T.; Kastritis, P. L.*, 2.7 Å cryo-EM structure of vitrified M. musculus H-chain apoferritin from 200 keV “screening microscope”. bioRxiv 2019, 738724. [Published in PLOS ONE, publication #40].