Publications

Publications with an asterisk (*) are considered highly relevant to our lab projects. Publications with 2 asterisks (**) are relevant for researching SARS-CoV-2.
Lab members are shown underlined

2024

• Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts.
  Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL*.
  Commun Biol, accepted.
• Protein-Rich Rafts in Hybrid Polymer/Lipid Giant Unilamellar Vesicles.
  Otrin N, Otrin L, Bednarz C, Träger TK, Hamdi F, Kastritis PL, Ivanov I, Sundmacher K.
  Biomacromolecules. 2024 Feb 12;25(2):778-791. doi: 10.1021/acs.biomac.3c00972.
  
• Effect of Molecular Dynamics and Internal Water Contact on the Photophysical Properties of Red pH-Sensitive Proteins.
  Schmitt FJ, Mehmood AS, Tüting C, Phan HT, Reisdorf J, Rieder F, Ghane Golmohamadi F, Verma R, Kastritis PL, Laufer J.
  Biochemistry. 2024 Jan 2;63(1):82-93. doi: 10.1021/acs.biochem.3c00444.
  

2023

• *Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote.
  Semchonok DA, Kyrilis FL, Hamdi F, Kastritis PL*.

  J Struct Biol X. 2023 Aug 9;8:100094. doi: 10.1016/j.yjsbx.2023.100094.
  

• *Enabling cryo-EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures.
  Tüting C, Schmidt L, Skalidis I, Sinz A, Kastritis PL*.
  Proteomics, 2023. e2200096. doi: 10.1002/pmic.202200096.
• Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and α-tocopherol.

  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.
  Nature Plants. 2023 Aug;9(8):1359-1369. doi: 10.1038/s41477-023-01483-0.
• The structural principles underlying molybdenum insertase complex assembly.

  Hassan AH, Ihling C, Iacobucci C, Kastritis PL, Sinz A, Kruse T.
  Protein Sci. 2023 Sep;32(9):e4753. doi: 10.1002/pro.4753.
• *Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon.
  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*.
  Commun Biol, 2023. 6(1):552. doi: 10.1038/s42003-023-04885-0.
• *Cracking the code of cellular protein-protein interactions: Alphafold and whole-cell crosslinking to the rescue.
  Träger T, Kastritis PL*. 
  Mol Syst Biol, 2023. 19(4):e11587. doi: 10.15252/msb.202311587.
• *IRAA: A statistical tool for investigating a protein–protein interaction interface from multiple structures.
  Belapure J, Sorokina M, Kastritis PL*.
  Protein Science, 2023. 32(1), e4523. doi: https://doi.org/10.1002/pro.4523
• *Enabling cryo-EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures.
  Tüting C, Schmidt L, Skalidis I, Sinz A, Kastritis PL*.
  Proteomics, 2023. e2200096. doi: 10.1002/pmic.202200096.
• Novel exotic alleles of EARLY FLOWERING 3 determine plant development in barley.
  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. 
  J Exp Bot, 2023. 74(12):3630-3650. doi: 10.1093/jxb/erad127
• Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans.
  Zhou Y, Syed JH, Semchonok DA, Wright E, Kyrilis FL, Hamdi F, Kastritis PL, Bruce BD, Reynolds TB.
  J Biol Chem, 2023. 299(6):104756. doi: 10.1016/j.jbc.2023.104756.
• Structural assessment of the full-length wild-type tumor suppressor protein p53 by mass spectrometry-guided computational modeling.
  Di Ianni A, Tüting C, Kipping M, Ihling CH, Köppen J, Iacobucci C, Arlt C, Kastritis PL, Sinz A.
  Scientific Reports, 2023. 13(1):8497. doi: 10.1038/s41598-023-35437-5.
• Encapsulation of cannabidiol in oil-in-water nanoemulsions and nanoemulsion-filled hydrogels: A structure and biological assessment study.
  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.
  Journal of Colloid and Interface Science, 2023. 634:300-313 doi: 10.1016/j.jcis.2022.12.036 

2022

• *Cryo-EM and artificial intelligence visualize endogenous protein community members. Skalidis, I., Kyrilis, F. L., Tüting, C., Hamdi, F., Chojnowski, G., & Kastritis, PL.
  Structure, 2022. S0969-2126(22)00001-6. https://doi.org/10.1016/j.str.2022.01.001
• Cryo-EM structure of the SEA complex.
  Tafur L, Hinterndorfer K, Gabus C, Lamanna C, Bergmann A, Sadian Y, Hamdi F, Kyrilis FL, Kastritis PL, Loewith R.
  Nature, 2022. 611, 399–404. https://doi.org/10.1038/s41586-022-05370-0
• *Cryo-electron microscopy snapshots of eukaryotic membrane proteins in native lipid-bilayer nanodiscs.
  Janson K, Kyrilis FL, Tüting C, Alfes M, Das M, Träger TK, Schmidt C, Hamdi F, Vargas C, Keller S, Meister A, Kastritis PL.
  Biomacromolecules, 2022 23(12), 5084-5094 DOI: 10.1021/acs.biomac.2c00935
• *An integrative approach to probing transient protein structures in cell extracts.
  Kastritis PL.
  Genetic Engineering & Biotechnology News, 2022. 42:9, 68-70
• *Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts.
  Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Shah PNM, Stubbs MT, Sinz A, Stuart DI, Kastritis PL .
  bioRxiv, 2022. 2022.07.15.498668; doi: https://doi.org/10.1101/2022.07.15.498668
• Filling the Gap with Long n-Alkanes: Incorporation of C20 and C30 into Phospholipid Membranes.
  Wurl  A, Ott M, Plato E, Meister A, Hamdi F, Kastritis PL, Blume A, Ferreira TM/
  Langmuir, 2022. https://doi.org/10.1021/acs.langmuir.2c00872
• **An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation.
  Sorokina M, Belapure J, Tüting C, Paschke R, Papasotiriou I, Rodrigues JPGLM, Kastritis PL.
  J Mol Biol, 2022. https://doi.org/10.1016/j.jmb.2022.167637
• Increased efficiency of charge-mediated fusion in polymer/lipid hybrid membranes.
  Marušič N, Otrin L, Rauchhaus J, Zhao Z, Kyrilis FL., Hamdi F, Kastritis PL, Dimova R, Ivanov I, Sundmacher K.
  Proc Natl Acad Sci U S A, 2022. https://doi.org/10.1073/pnas.2122468119
• Investigating bolalipids as solubilizing agents for poorly soluble drugs: Effects of alkyl chain length on solubilization and cytotoxicity.
  Li F, Harvey RD, Modicano P, Hamdi F, Kyrilis FL, Müller S, Gruhle K, Kastritis PL, Drescher S, Dailey LA.
  Colloids and Surfaces B: Biointerfaces, 2022. https://doi.org/10.1016/j.colsurfb.2022.112369
• *Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium.
  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.
  Plant Communications, 2022. https://doi.org/10.1016/j.xplc.2021.100248
• Osmotic stress response in BetP: How lipids and K⁺ team up to overcome downregulation
  Heinz V, Güler G, Leone V, Madej MG, Maksimov S, Gärtner RM, Rudi O, Hamdi F, Kastritis PL, Mäntele W, Krämer R, Forrest LR, Perez C, Ziegler C bioRxiv, 2022. 2022.06.02.493408; doi: https://doi.org/10.1101/2022.06.02.493408

2021

• *Cryo-EM snapshots of a native lysate provide structural insights into a metabolon-embedded transacetylase reaction.
  Tüting C, Kyrilis FL, Müller J, Sorokina M, Skalidis I, Hamdi F, Sadian Y, Kastritis PL*.
  Nature Communications, 2021. 12(1): 6933. https://doi.org/10.1038/s41467-021-27287-4
• Nanoscale Model System for the Human Myelin Sheath.
  Hoffmann M, Haselberger D, Hofmann T, Müller L, Janson K, Meister A, Das M, Vargas C, Keller S, Kastritis PL, Schmidt C, & Hinderberger D.
  Biomacromolecules, 2021. 22(9), 3901–3912. https://doi.org/10.1021/acs.biomac.1c00714
• Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons.
  Piersimoni L, Kastritis PL, Arlt C. & Sinz A.
  Chemical Reviews, 2021. https://doi.org/10.1021/acs.chemrev.1c00786
• BRCA1-BRCT Mutations Alter the Subcellular Localization of BRCA1 In Vitro.
  Drikos I, Boutou E, Kastritis P L, & Vorgias CE.
  Anticancer research, 2021. 41(6), 2953–2962. https://doi.org/10.21873/anticanres.15077
• Thin-Layer Chromatography and Coomassie Staining of Phospholipids for Fast and Simple Lipidomics Sample Preparation.
  Hofmann T, Barth M, Meister A, Kastritis PL, Schmidt C.
  Analysis & Sensing, 2021, 1:171. https://doi.org/10.1002/anse.202100029
• En route to dynamic life processes by SNARE-mediated fusion of polymer and hybrid membranes.
  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 .
  Nature Communications, 2021. 12(1): 4972. https://doi.org/10.1038/s41467-021-25294-z
• *Solubilization of artificial mitochondrial membranes by amphiphilic copolymers of different charge.
  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.
  Biochim Biophys Acta Biomembr, 2021. 1863(12): 183725. https://doi.org/10.1016/j.bbamem.2021.183725
• *Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilum
  Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, et al.
  PLOS ONE, 2021. 16(7): e0254429. https://doi.org/10.1371/journal.pone.0254429
• ***Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts.
  Kyrilis FL#, Semchonok DA#, Skalidis I, Tüting C, Hamdi F, O’Reilly FJ, Rappsilber J, Kastritis PL*.
  Cell Rep., 2021. 34(6):108727. doi: 10.1016/j.celrep.2021.108727.
• *Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist’s Perspective.
  Kyrilis FL, Belapure J, Kastritis PL*
  Front Mol Biosci. 2021. 8:229. doi: 10.3389/fmolb.2021.660542.
• First 3D-Structural Data of Full-length Guanylyl Cyclase 1 in Rod-Outer-Segment Preparations of Bovine Retina by Cross-linking/Mass Spectrometry.
  Rehkamp A, Tänzler D, Tüting C, Kastritis PL, Iacobucci C, Ihling CH, Kipping M, Koch KW, Sinz A*.
  J Mol Biol. 2021. 433(10):166947. doi: 10.1016/j.jmb.2021.166947
• Algorithmic robustness to preferred orientations in Single Particle Analysis by CryoEM.
  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*.
  J Struct Biol. 2021. 213(1):107695. doi: 10.1016/j.jsb.2020.107695.

2020

• **Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design.
  Sorokina M, M C Teixeira J, Barrera-Vilarmau S, Paschke R, Papasotiriou I, Rodrigues JPGLM, Kastritis PL*
  Scientific Data. 2020. 7(1):309. doi: 10.1038/s41597-020-00652-6.
• Cryo-EM Structure of a Tetrameric Photosystem I from Chroococcidiopsis TS-821, a Thermophilic, Non-heterocyst-forming Cyanobacteria.
  Semchonok D#, Mondal J#, Cooper C, Schlum K, Li M, Amin M, Sorzano CS, Ramírez-Aportela E, Kastritis PL, Boekema E, Guskov A, Bruce B*
  [preprint @Research Square doi: 10.21203/rs.3.rs-81702/v1 PPR: PPR227494]
• *Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
  Zhou Y#, Kastritis PL#*, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen W, Förster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A*, Silva GM*
  Proc Natl Acad Sci U S A. 2020. Aug 27:202005301. doi: 10.1073/pnas.2005301117
• Enhanced optical imaging properties of lipid nanocapsules as vehicles for fluorescent conjugated polymers.
  Modicano P, Neumann R, Schüller M, Holthof J, Kyrilis FL, Hamdi F, Kastritis PL, Mäder K, Dailey LA*
  Eur J Pharm Biopharm. 2020 Sep;154:297-308. doi: 10.1016/j.ejpb.2020.07.017.
• *Unstructured regions of large enzymatic complexes control the availability of metabolites with signaling functions.
  Skalidis I, Tüting C, Kastritis PL*
  Cell Commun. Signal. 2020. Aug 26;18(1):136. doi: 10.1186/s12964-020-00631-9.
• *Structural analysis of 70S ribosomes by cross-Linking/mass Spectrometry reveals conformational plasticity.
  Tüting C, Iacobucci C, Ihling CE, Kastritis PL*, Sinz A*
  Sci Rep. 2020. Jul 28;10(1):12618. doi: 10.1038/s41598-020-69313-3.
• Constructing artificial respiratory chain in polymer compartments: Insights into the interplay between bo3 oxidase and the membrane.
  Marušič N, Otrin L, Zhao Z, Lira RB, Kyrilis FL, Hamdi F, Kastritis PL, Vidaković-Koch T, Ivanov I, Sundmacher K, Dimova R.
  Proc Natl Acad Sci U S A. 2020 117(26):15006-15017. doi: 10.1073/pnas.1919306117
• **Insights on cross-species transmission of SARS-CoV-2 from structural modeling.
  Rodrigues PGLM J*, Barrera-Vilarmau S, Texeira MC J, Seckel E, Kastritis PL, Levitt M.
  PLoS computational biology 2020. 16(12), e1008449
  [preprint was @BioRxiv 2020 2020.06.05.136861. doi: 10.1101/2020.06.05.136861]
• *2.7 Å cryo-EM structure of vitrified M. musculus H-chain apoferritin from a compact 200 keV cryo-microscope.
  Hamdi F, Tüting C, Semchonok DA, Kyrilis FL, Meister A, Skalidis I, Schmidt L, Parthier C, Stubbs MT*, Kastritis PL*
  PLOS One. 2020. 15(5): e0232540.
  [preprint was @BioRxiv 2019 738724. doi: 10.1101/738724]
• Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies.
  Niemeyer M, Castillo EM, Ihling CH, Iacobucci C, Wilde V, Hellmuth A, Hoehenwarter W, Samodelov SL, Zurbriggen MD, Kastritis PL, Sinz A & Villalobos LIAC.
  Nature Communications. 2020. 11, 2277.
  [preprint was @BioRxiv 2019 787770. doi: 10.1101/787770]

2019

• *Integrative biology of native cell extracts: a new era for structural characterization of life processes.
  Kyrilis FL, Meister A, Kastritis PL*.
  Biol Chem. 2019 Jun 26;400(7):831-846. doi: 10.1515/hsz-2018-0445.
• Structure and Assembly of the Nuclear Pore Complex.
  Hampoelz B, Andres-Pons A, Kastritis PL, Beck M.
  Annu Rev Biophys. 2019 Apr 3. doi: 10.1146/annurev-biophys-052118-115308.

2018

• *Enzymatic complexes across scales.
  Kastritis PL, Gavin AC.
  Essays Biochem. 2018 Oct 26;62(4):501-514. doi: 10.1042/EBC20180008. Print 2018 Oct 26.
• Defining distance restraints in HADDOCK.
  Bonvin AM, Karaca E, Kastritis PL, Rodrigues JP.
  Nat Protoc. 2018 Jul;13(7):1503. doi: 10.1038/s41596-018-0017-6. Epub 2018 Jun 25. No abstract available.

2017

• *Capturing protein communities by structural proteomics in a thermophilic eukaryote.
  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.
  Mol Syst Biol. 2017 Jul 25;13(7):936. doi: 10.15252/msb.20167412.
• Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins.
  Ichikawa M, Liu D, Kastritis PL, Basu K, Hsu TC, Yang S, Bui KH.
  Nature Communications. 2017 May 2;8:15035. doi: 10.1038/ncomms15035.
• Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.
  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.
  Proteins. 2017 Mar;85(3):417-423. doi: 10.1002/prot.25198. Epub 2016 Nov 24. Erratum in: Proteins. 2017 Aug;85(8):1589-1590.

2016

• *The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
  van Zundert GCP, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AM.
  J Mol Biol. 2016 Feb 22;428(4):720-725. doi: 10.1016/j.jmb.2015.09.014. Epub 2015 Sep 26.
• dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.
  Spiliotopoulos D, Kastritis PL, Melquiond AS, Bonvin AM, Musco G, Rocchia W, Spitaleri A.
  Front Mol Biosci. 2016 Aug 31;3:46. doi: 10.3389/fmolb.2016.00046. eCollection 2016.
• PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
  Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A.
  Bioinformatics. 2016 Dec 1;32(23):3676-3678. Epub 2016 Aug 8.
• Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
  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.
  Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.
• New potential peptide therapeutics perturbing CK1δ/α-tubulin interaction.
  Krüger M, Kalbacher H, Kastritis PL, Bischof J, Barth H, Henne-Bruns D, Vorgias C, Sarno S, Pinna LA, Knippschild U.
  Cancer Lett. 2016 Jun 1;375(2):375-383. doi: 10.1016/j.canlet.2016.03.021. Epub 2016 Mar 17.
• Spatiotemporal variation of mammalian protein complex stoichiometries.
  Ori A, Iskar M, Buczak K, Kastritis PL, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M.
  Genome Biol. 2016 Mar 14;17:47. doi: 10.1186/s13059-016-0912-5.
• The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex.
  Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis PL, Bork P, Beck M, Müller CW.
  PLoS One. 2016 Jan 8;11(1):e0146457. doi: 10.1371/journal.pone.0146457. eCollection 2016.

2015

• *Non-interacting surface solvation and dynamics in protein-protein interactions.
  Visscher KM, Kastritis PL, Bonvin AM.
  Proteins. 2015 Mar;83(3):445-58. doi: 10.1002/prot.24741. Epub 2015 Jan 21.
• In situ structural analysis of the human nuclear pore complex.
  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.
  Nature. 2015 Oct 1;526(7571):140-143. doi: 10.1038/nature15381. Epub 2015 Sep 23.
• Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
  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.
  J Mol Biol. 2015 Sep 25;427(19):3031-41. doi: 10.1016/j.jmb.2015.07.016. Epub 2015 Jul 29.
• Structural basis for assembly and function of the Nup82 complex in the nuclear pore scaffold.
  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.
  J Cell Biol. 2015 Feb 2;208(3):283-97. doi: 10.1083/jcb.201411003.

2014

• *Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface.
  Kastritis PL, Rodrigues JP, Folkers GE, Boelens R, Bonvin AM.
  J Mol Biol. 2014 Jul 15;426(14):2632-52. doi: 10.1016/j.jmb.2014.04.017. Epub 2014 Apr 25.
• An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.
  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.
  Nucleic Acids Res. 2014 Dec 16;42(22):13525-33. doi: 10.1093/nar/gku1147. Epub 2014 Nov 14.
• HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors.
  Kastritis PL, Rodrigues JP, Bonvin AM.
  J Chem Inf Model. 2014 Mar 24;54(3):826-36. doi: 10.1021/ci4005332. Epub 2014 Feb 27.
• Blind prediction of interfacial water positions in CAPRI.
  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.
  Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23.

2013

• *Molecular origins of binding affinity: seeking the Archimedean point.
  Kastritis PL, Bonvin AM.
  Curr Opin Struct Biol. 2013 Dec;23(6):868-77. doi: 10.1016/j.sbi.2013.07.001. Epub 2013 Jul 19. Review.
• Defining the limits of homology modeling in information-driven protein docking.
  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.
  Proteins. 2013 Dec;81(12):2119-28. doi: 10.1002/prot.24382. Epub 2013 Oct 17.
• Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
  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.
  Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.
• Solvated protein-DNA docking using HADDOCK.
  van Dijk M, Visscher KM, Kastritis PL, Bonvin AM.
  J Biomol NMR. 2013 May;56(1):51-63. doi: 10.1007/s10858-013-9734-x. Epub 2013 Apr 30.
• Solvated protein-protein docking using Kyte-Doolittle-based water preferences.
  Kastritis PL, Visscher KM, van Dijk AD, Bonvin AM.
  Proteins. 2013 Mar;81(3):510-8. doi: 10.1002/prot.24210. Epub 2012 Dec 24.
• HADDOCK.
  Bonvin AM, van Dijk M, Karaca E, Kastritis PL, Melquiond ASJ, Schmitz C, de Vries SJ.
  Encyclopedia of Biophysics, Springer. 2013 943-944. doi:10.1007/978-3-642-16712-6_330

2012

• *On the binding affinity of macromolecular interactions: daring to ask why proteins interact.
  Kastritis PL, Bonvin AM.
  J R Soc Interface. 2012 Dec 12;10(79):20120835. doi: 10.1098/rsif.2012.0835. Print 2013 Feb. Review.
• Clustering biomolecular complexes by residue contacts similarity.
  Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, Bonvin AM.
  Proteins. 2012 Jul;80(7):1810-7. doi: 10.1002/prot.24078. Epub 2012 May 8.
• Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.
  Kastritis PL, van Dijk AD, Bonvin AM.
  Methods Mol Biol. 2012;819:355-74. doi: 10.1007/978-1-61779-465-0_22.
• Next challenges in protein–protein docking: from proteome to interactome and beyond.
  Melquiond AS, Karaca E, Kastritis PL, Bonvin AM.
  WIRES Comput Mol Sci. 2012;2:642-651. doi: 10.1002/wcms.91
• Predicting and dissecting high-order molecular complexity by Information-driven Biomolecular Docking
  Kastritis PL & Bonvin AM.
  Antimicrobial Drug Discovery: Emerging Strategies. 2012; 22:232246.
• Protein-protein docking with HADDOCK.

  Schmitz C, Melquiond ASJ, de Vries SJ, Karaca E, van Dijk M, Kastritis PL, Bonvin AM.
  NMR of biomolecules: towards mechanistic systems biology. 2012;520-535. doi: 10.1002/9783527644506.ch32

2011

• *A structure-based benchmark for protein-protein binding affinity.
  Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J.
  Protein Sci. 2011 Mar;20(3):482-91. doi: 10.1002/pro.580. Epub 2011 Feb 16.
• Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
  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, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D.
  J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29.
• Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria.
  Fiamegos YC, Kastritis PL, Exarchou V, Han H, Bonvin AM, Vervoort J, Lewis K, Hamblin MR, Tegos GP.
  PLoS One. 2011 Apr 4;6(4):e18127. doi: 10.1371/journal.pone.0018127.

2010

• Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.
  de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM.
  Proteins. 2010 Nov 15;78(15):3242-9. doi: 10.1002/prot.22814.
• Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark.
  Kastritis PL, Bonvin AM.
  J Proteome Res. 2010 May 7;9(5):2216-25. doi: 10.1021/pr9009854. Erratum in: J Proteome Res. 2011 Feb 4;10(2):921-2.
• Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.
  Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM.
  Mol Cell Proteomics. 2010 Aug;9(8):1784-94. doi: 10.1074/mcp.M000051-MCP201. Epub 2010 Mar 19.

2007

• Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs.
  Kastritis PL, Papandreou NC, Hamodrakas SJ.
  Int J Biol Macromol. 2007 Oct 1;41(4):447-53. Epub 2007 Jun 19.