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.

2020

2019

2018

2017

2016

2015

2014

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

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

2007