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Staff at EMBL

Panagiotis Kastritis

Postdoctoral Fellow (EIPOD)
Beck Group Gavin Group

EMBL Heidelberg, Meyerhofstra├če 1, 69117 Heidelberg, Germany

Tel: +49 6221 387-8107
E-mail: send a mail

Publications

Proteins feel more than they see: Fine-tuning of binding affinity by properties of the non-interacting surface. Kastritis, P.L., Rodrigues, J.P., Folkers, G.E., Boelens, R. & Bonvin, A.M. J Mol Biol. 2014 Apr 24. pii: S0022-2836(14)00201-0. doi:10.1016/j.jmb.2014.04.017. Europe PMC

HADDOCK2P2I: A robust biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. Kastritis, P.L., Rodrigues, J.P. & Bonvin, A.M. J Chem Inf Model. 2014 Feb 12. Europe PMC

Defining the limits of homology modeling in information-driven protein docking. Rodrigues, J.P., Melquiond, A.S., Karaca, E., Trellet, M., van Dijk, M., van Zundert, G.C., Schmitz, C., de Vries, S.J., Bordogna, A., Bonati, L., Kastritis, P.L. & Bonvin, A.M. Proteins. 2013 Dec;81(12):2119-28. doi: 10.1002/prot.24382. Epub 2013 Oct 17. Europe PMC

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Moretti, R., Fleishman, S.J., Agius, R., Torchala, M., Bates, P.A., Kastritis, P.L., Rodrigues, J.P., Trellet, M., Bonvin, A.M., 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, J.J., Popov, P., Grudinin, S., Esquivel-Rodriguez, J., Kihara, D., Zhao, N., Korkin, D., Zhu, X., Demerdash, O.N., Mitchell, J.C., Kanamori, E., Tsuchiya, Y., Nakamura, H., Lee, H., Park, H., Seok, C., Sarmiento, J., Liang, S., Teraguchi, S., Standley, D.M., Shimoyama, H., Terashi, G., Takeda-Shitaka, M., Iwadate, M., Umeyama, H., Beglov, D., Hall, D.R., Kozakov, D., Vajda, S., Pierce, B.G., Hwang, H., Vreven, T., Weng, Z., Huang, Y., Li, H., Yang, X., Ji, X., Liu, S., Xiao, Y., Zacharias, M., Qin, S., Zhou, H.X., Huang, S.Y., Zou, X., Velankar, S., Janin, J., Wodak, S.J. & Baker, D. Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23. Europe PMC

Blind prediction of interfacial water positions in CAPRI. Lensink, M.F., Moal, I.H., Bates, P.A., Kastritis, P.L., Melquiond, A.S., Karaca, E., Schmitz, C., van Dijk, M., Bonvin, A.M., Eisenstein, M., Jimenez-Garcia, B., Grosdidier, S., Solernou, A., Perez-Cano, L., Pallara, C., Fernandez-Recio, J., Xu, J., Muthu, P., Praneeth Kilambi, K., Gray, J.J., Grudinin, S., Derevyanko, G., Mitchell, J.C., Wieting, J., Kanamori, E., Tsuchiya, Y., Murakami, Y., Sarmiento, J., Standley, D.M., Shirota, M., Kinoshita, K., Nakamura, H., Chavent, M., Ritchie, D.W., Park, H., Ko, J., Lee, H., Seok, C., Shen, Y., Kozakov, D., Vajda, S., Kundrotas, P.J., Vakser, I.A., Pierce, B.G., Hwang, H., Vreven, T., Weng, Z., Buch, I., Farkash, E., Wolfson, H.J., Zacharias, M., Qin, S., Zhou, H.X., Huang, S.Y., Zou, X., Wojdyla, J.A., Kleanthous, C. & Wodak, S.J. Proteins. 2013 Oct 23. doi: 10.1002/prot.24439. Europe PMC

Molecular origins of binding affinity: seeking the Archimedean point. Kastritis, P.L. & Bonvin, A.M. Curr Opin Struct Biol. 2013 Jul 19. pii: S0959-440X(13)00121-8. doi:10.1016/j.sbi.2013.07.001. Europe PMC

Solvated protein-DNA docking using HADDOCK. van Dijk, M., Visscher, K.M., Kastritis, P.L. & Bonvin, A.M. J Biomol NMR. 2013 May;56(1):51-63. doi: 10.1007/s10858-013-9734-x. Epub 2013 Apr30. Europe PMC

Solvated protein-protein docking using Kyte-Doolittle-based water preferences. Kastritis, P.L., Visscher, K.M., van Dijk, A.D. & Bonvin, A.M. Proteins. 2013 Mar;81(3):510-8. doi: 10.1002/prot.24210. Epub 2012 Dec 24. Europe PMC

On the binding affinity of macromolecular interactions: daring to ask why proteins interact. Kastritis, P.L. & Bonvin, A.M. J R Soc Interface. 2012 Dec 12;10(79):20120835. doi: 10.1098/rsif.2012.0835.Print 2013 Feb. Europe PMC

Clustering biomolecular complexes by residue contacts similarity. Rodrigues, J.P., Trellet, M., Schmitz, C., Kastritis, P., Karaca, E., Melquiond, A.S. & Bonvin, A.M. Proteins. 2012 Jul;80(7):1810-7. doi: 10.1002/prot.24078. Epub 2012 May 8. Europe PMC

Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach. Kastritis, P.L., van Dijk, A.D. & Bonvin, A.M. Methods Mol Biol. 2012;819:355-74. doi: 10.1007/978-1-61779-465-0_22. Europe PMC

Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Fleishman, S.J., Whitehead, T.A., Strauch, E.M., Corn, J.E., Qin, S., Zhou, H.X., Mitchell, J.C., Demerdash, O.N., Takeda-Shitaka, M., Terashi, G., Moal, I.H., Li, X., Bates, P.A., Zacharias, M., Park, H., Ko, J.S., Lee, H., Seok, C., Bourquard, T., Bernauer, J., Poupon, A., Aze, J., Soner, S., Ovali, S.K., Ozbek, P., Tal, N.B., Haliloglu, T., Hwang, H., Vreven, T., Pierce, B.G., Weng, Z., Perez-Cano, L., Pons, C., Fernandez-Recio, J., Jiang, F., Yang, F., Gong, X., Cao, L., Xu, X., Liu, B., Wang, P., Li, C., Wang, C., Robert, C.H., 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, D.M., Nakamura, H., Kinoshita, K., Driggers, C.M., Hall, R.G., Morgan, J.L., Hsu, V.L., Zhan, J., Yang, Y., Zhou, Y., Kastritis, P.L., Bonvin, A.M., Zhang, W., Camacho, C.J., Kilambi, K.P., Sircar, A., Gray, J.J., Ohue, M., Uchikoga, N., Matsuzaki, Y., Ishida, T., Akiyama, Y., Khashan, R., Bush, S., Fouches, D., Tropsha, A., Esquivel-Rodriguez, J., Kihara, D., Stranges, P.B., Jacak, R., Kuhlman, B., Huang, S.Y., Zou, X., Wodak, S.J., Janin, J. & Baker, D. J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011Sep 29. Europe PMC

Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria. Fiamegos, Y.C., Kastritis, P.L., Exarchou, V., Han, H., Bonvin, A.M., Vervoort, J., Lewis, K., Hamblin, M.R. & Tegos, G.P. PLoS One. 2011 Apr 4;6(4):e18127. doi: 10.1371/journal.pone.0018127. Europe PMC

A structure-based benchmark for protein-protein binding affinity. Kastritis, P.L., Moal, I.H., Hwang, H., Weng, Z., Bates, P.A., Bonvin, A.M. & Janin, J. Protein Sci. 2011 Mar;20(3):482-91. doi: 10.1002/pro.580. Epub 2011 Feb 16. Europe PMC

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions. de Vries, S.J., Melquiond, A.S., Kastritis, P.L., Karaca, E., Bordogna, A., van Dijk, M., Rodrigues, J.P. & Bonvin, A.M. Proteins. 2010 Nov 15;78(15):3242-9. doi: 10.1002/prot.22814. Europe PMC

Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Karaca, E., Melquiond, A.S., de Vries, S.J., Kastritis, P.L. & Bonvin, A.M. Mol Cell Proteomics. 2010 Aug;9(8):1784-94. doi: 10.1074/mcp.M000051-MCP201. Epub2010 Mar 19. Europe PMC

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. Kastritis, P.L. & Bonvin, A.M. J Proteome Res. 2010 May 7;9(5):2216-25. doi: 10.1021/pr9009854. Europe PMC

Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs. Kastritis, P.L., Papandreou, N.C. & Hamodrakas, S.J. Int J Biol Macromol. 2007 Oct 1;41(4):447-53. Epub 2007 Jun 19. Europe PMC