Nazar Zaki
Associate Professor and Coordinator











Positions: Research Assistant (or Postdoc) available

To apply please send your CV to Dr. Nazar Zaki (




Software, data and supplementary materials:

DyCluster: Supplementary Materials
Detecting protein complexes in protein interaction networks modeled as gene expression biclusters

Data and codes

SVM-Net: Supplementary Materials
Multi-protein complex detection by integrating network topological features and biological process information


TRIBAL: Supplementary Materials
Nazar Zaki and Antonio Mora (2014) A comparative analysis of computational approaches and algorithms for protein subcomplex identification. Scientific Reports, 4: 4262. Nature Group.

Supplementary File, Code1, Code2


CISA: Supplementary Materials
Maad Shatnawi & Nazar Zaki (submitted) "Inter-domain linker prediction using simulated annealing".

Data and Codes

Nested Complexes: Supplementary Materials
Nazar Zaki & Antonio Mora (Accepted) "".

Code, Data


ProRank+: Supplementary Materials
Eileen Hana & Nazar Zaki (
Submitted) "Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure".

Data, Codes


PEWCC: Supplementary Materials
Nazar Zaki, Dmitry Efimov & Jose Berengueres (2013) "Protein Complex Detection using Interaction Reliability Assessment and Weighted Clustering Coefficient". BMC Bioinformatics, 14:163.

Code , Data


ProRank: Supplementary Materials
Nazar Zaki, Jose Berengueres, Dmitry Efimov (2012). "Detection of protein complexes using a protein ranking algorithm". Proteins, 80(10): 2459-68, 2012. Wiley

ProRank-0.1SimMat Data  Results  ReadMe 


TMHindex: Supplementary Materials
Nazar Zaki, Salah Bouktif, Sanja L., (2011) "A Combination of Compositional Index and Genetic Algorithm for Predicting Transmembrane Helical Segments". PLoS ONE 6(7): e21821. doi:10.1371/journal.pone.0021821.

DATASET-1 (test_seq), DATASET-2 (test_seq)
Compositional Index and GA
Predictions on DATASET-1, Predictions on DATASET-2, Comparisons


SVM-Freescore: Supplementary Materials
Nazar Zaki, Stefan Wolfsheimer, Gregory Nuel, Sawsan Khuri (2011) "Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines", BMC Bioinformatics 2011, 12:217

Freescore, LIBSVM



STRIKE: Supplementary Materials
Nazar Zaki, Wassim M El-Hajj, Hesham Kamel, Fadi Sibai (2011) "STRIKE: A Protein-Protein Interaction Classification Approach". Advances in Experimental Medicine and Biology , Vol. 696, pp: 263-70., Springer.

The tool runs under windows platform (cygwin).



PPI-PS: Supplementary Materials
Nazar Zaki, Sanja L Lazarova-Molnar, Wassim M El-Hajj, Piers Campbell (2009), "Protein-protein interaction based on pairwise similarity". BMC Bioinformatics. 10:150.

Data and source codes (Exp. no. 1, 3 and 4),  Data and source codes (Exp. no. 2)