EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Tel: +49 6221 387-8107

E-mail: Send a mail

Publications

Total: 23 publication(s)

2015

Visscher KM, Kastritis PL, Bonvin AM. (2015)

Non-interacting surface solvation and dynamics in protein-protein interactions.

Proteins 83(3):445-458. doi:10.1002/prot.24741
Europe PMC | doi

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. (2015)

Structural basis for assembly and function of the Nup82 complex in the nuclear pore scaffold.

J. Cell Biol. 208(3):283-297. doi:10.1083/jcb.201411003
Europe PMC | doi


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. (2014)

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Nucleic Acids Res. 42(22):13525-13533. doi:10.1093/nar/gku1147
Europe PMC | doi

Kastritis PL, Rodrigues JP, Folkers GE, Boelens R, Bonvin AM. (2014)

Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface

J. Mol. Biol. 426(14):2632-2652. doi:10.1016/j.jmb.2014.04.017
Europe PMC | doi

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. (2014)

Blind prediction of interfacial water positions in CAPRI

Proteins 82(4):620-632. doi:10.1002/prot.24439
Europe PMC | doi

Kastritis PL, Rodrigues JP, Bonvin AM. (2014)

HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors

J Chem Inf Model 54(3):826-836. doi:10.1021/ci4005332
Europe PMC | doi


2013

Kastritis PL, Bonvin AM. (2013)

Molecular origins of binding affinity: seeking the Archimedean point

Curr. Opin. Struct. Biol. 23(6):868-877. doi:10.1016/j.sbi.2013.07.001
Europe PMC | doi

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. (2013)

Defining the limits of homology modeling in information-driven protein docking

Proteins 81(12):2119-2128. doi:10.1002/prot.24382
Europe PMC | doi

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. (2013)

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Proteins 81(11):1980-1987. doi:10.1002/prot.24356
doi

van Dijk M, Visscher KM, Kastritis PL, Bonvin AM. (2013)

Solvated protein-DNA docking using HADDOCK

J. Biomol. NMR 56(1):51-63. doi:10.1007/s10858-013-9734-x
Europe PMC | doi

Kastritis PL, Visscher KM, van Dijk AD, Bonvin AM. (2013)

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

Proteins 81(3):510-518. doi:10.1002/prot.24210
Europe PMC | doi

Kastritis PL, Bonvin AM. (2013)

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

J R Soc Interface 10(79):20120835. doi:10.1098/rsif.2012.0835
Europe PMC | doi

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E at al. (2013)

Blind prediction of interfacial water positions in CAPRI

Proteins 82(4):620-632. doi:10.1002/prot.24439
doi

Rodrigues JPGLM, Melquiond ASJ, Karaca E, Trellet M, van Dijk M, Zundert GCP, Schmitz C, Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AMJJ. (2013)

Defining the limits of homology modeling in information‐driven protein docking

Proteins doi:10.1002/prot.24382
doi


2012

Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. (2012)

Clustering biomolecular complexes by residue contacts similarity

Proteins 80(7):1810-1817. doi:10.1002/prot.24078
Europe PMC | doi

Kastritis PL, van Dijk AD, Bonvin AM. (2012)

Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach

Methods Mol. Biol. 819:355-374. doi:10.1007/978-1-61779-465-0_22
Europe PMC | doi


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, 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. (2011)

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

J. Mol. Biol. 414(2):289-302. doi:10.1016/j.jmb.2011.09.031
Europe PMC | doi

Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J. (2011)

A structure-based benchmark for protein-protein binding affinity

Protein Sci. 20(3):482-491. doi:10.1002/pro.580
Europe PMC | doi

Fiamegos YC, Kastritis PL, Exarchou V, Han H, Bonvin AM, Vervoort J, Lewis K, Hamblin MR, Tegos GP. (2011)

Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria

PLoS ONE 6(4):e18127. doi:10.1371/journal.pone.0018127
Europe PMC | doi


2010

de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM. (2010)

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions

Proteins 78(15):3242-3249. doi:10.1002/prot.22814
Europe PMC | doi

Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM. (2010)

Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server

Mol. Cell Proteomics 9(8):1784-1794. doi:10.1074/mcp.m000051-mcp201
Europe PMC | doi

Kastritis PL, Bonvin AM. (2010)

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark

J. Proteome Res. 9(5):2216-2225. doi:10.1021/pr9009854
Europe PMC | doi


2007

Kastritis PL, Papandreou NC, Hamodrakas SJ. (2007)

Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs

Int. J. Biol. Macromol. 41(4):447-453. doi:10.1016/j.ijbiomac.2007.06.005
Europe PMC | doi