Members

Principal  Investigators

Attila Gürsoy

Principal Investigator
Research Area
Computational Biology

For more information see Dr. Gursoy’s home page.

Özlem Keskin

Principal Investigator
Research
Computational Biology

For more information see Dr. Keskin’s homepage.

PhD Students

Jackson Weako

Jackson Weako

PhD Candidate in Computational Science and Engineering
Research


Short Bio

Ph.D. Candidate Koç University-

M.Sc.  Kadir Has University-Computational Biology and Bioinformatics

B.Sc. Cuttington University-Chemistry

For more information see Jackson’s homepage

Meryem Eren

PhD Student in Molecular Biology and Genetics
Short Bio
Ph.D. Student Koç University – Molecular Biology and Genetics
B.Sc. Istanbul Technical University – Molecular Biology and Genetics

Irşad Ferhat

PhD Student in Computational Science

MSc Students

Damla Övek

MSc Candidate in Computational Science and Engineering
Research
Proteins bind together via their interface. Some residues on the interface regions, play more important role than other residues in terms of contribution to binding. We call those residues “hotspots”. Considering their roles in binding, hotspots might be very promising drug targets for inhibition of unwanted protein interactions. My study is about the improvement of our hotspot prediction server called HotPoint.

Short Bio

M.Sc. Candidate Koç University-Computational Science & Engineering

B.Sc. Koç University-Molecular Biology & Genetics

B.Sc. Koç University-Computer Engineering (Double Major)

For more information see Damla’s homepage

Sosyorol-Sosyal İçerik Platformu

Kayra Kösoğlu

MSc Student in Molecular Biology and Genetics
Research
Proteins bind together via their interface. Some residues on the interface regions, play more important role than other residues in terms of contribution to binding. We call those residues “hotspots”. Considering their roles in binding, hotspots might be very promising drug targets for inhibition of unwanted protein interactions. My aim is to accurately predict hotspot residues by enhancing current detection algorithms.

Short Bio

M.Sc. Student Koç University-Molecular Biology and Genetics

B.Sc. Istanbul Bilgi University-Genetics and Bio-engineering

Zeynep Abalı

MSc Student in Data Science

Sukejna Valjevac

MSc Student in Computer Science and Engineering
Research
 Protein Interfaces

Short Bio

M.Sc. Student Koç University-Computer Science & Engineering

B.Sc. Boğaziçi University-Molecular Biology &Genetics

Simge Şenyüz

MSc Student in Computational Science
Short Bio

M.Sc. Student Koç University-Computational Science

B.Sc. Boğaziçi University-Chemistry

Yunus Emre Köroğlu

MSc Student in Data Science
Short Bio

M.Sc. Student Koç University-Data Science

B.Sc. Boğaziçi University-Chemistry (Double Major)

B.Sc. Boğaziçi University-Molecular Biology and Genetics

Emre Küçük

MSc Student in Data Science
Short Bio

M.Sc. Student Koç University-Data Science

B.Sc. Istanbul Technical University-Mathematical Engineering

Undergrad Students

Alumni

Recent

Ayşe Derya Cavga

PhD in Chemical and Biological Engineering

Research
Identification and Structural Modelling of the Protein Interactors of A Long Non-coding RNA Involved in Prostate Cancer

Prostate cancer affects 1 in 7 men. A long non-coding RNA acts as an enhancer and influences transcription of the Kallikrein gene family involved in prostate cancer.  My main project aims to identify the protein partners of this lncRNA and structurally model the complex they form.

Side Projects:

  • Structural analysis of the oligomerization & interactions of the steroid hormone glucocorticoid receptor
  • RNA-Sequencing Analysis of Cryptochrome mutation in a p53 knockout background
Short Bio
B.Sc. Bilkent University-Molecular Biology and Genetics
M.Sc. Bilkent University-Molecular Biology and Genetics
Ph.D. Koç University-Chemical and Biological Engineering

Ali Tuğrul Balcı

MSc in Computer Science and Engineering
Research
Protein-Protein Interaction Using Statistical and Deterministic Algorithms

Since proteins are pivotal for the most of the crucial activities that are happening in organisms and the proteins, most of the time, do not act alone, studying protein-protein interactions is very important. Predicting which proteins can interact with each other is a very valuable skill on which I am working by using both statistical and deterministic algorithms.

Short Bio
B.Sc. Istanbul Technical University-Computer Engineering
M.Sc. Koç University-Computer Science and Engineering

Ayşe Seda Yazgılı

MSc in Molecular Biology and Genetics
Research
Molecular Dynamics Simulations and Computational Analysis of KRAS and c-Raf Interaction

Ras  protein is shown to interact with the proteins involved in crucial pathways such as MAPK and PI3K. Our group recently showed that specific mutations on Ras protein interfere with the p-ERK level within the cell. Using molecular dynamics simulation methods and computational analysis, we aim to have a deeper understanding how these mutations affects the interaction .Therefore, I am simulating the interactions of KRAS protein and Ras-Binding-Domain (RBD) of c-Raf protein.

Short Bio

M.Sc. Koç University-Molecular Biology and Genetics

B.Sc. İstanbul Technical University-Molecular Biology and Genetics

For more information see Ayşe Seda’s homepage

Berna Özer

PhD in Molecular Biology and Genetics
Research
Molecular Dynamic Simulations and Computational Analysis of KRAS Dimerization

The function of the Ras proteins is the recruitment and activation of the effectors which play role  in cell signalling. Recent studies show that Ras can dimerize using two interfaces; α homodimer and β homodimer. We aim to create a mutation in α homodimer and show the effect of the mutation on the Ras dimerization.

 

Short Bio

Ph.D. Koç University-Molecular Biology and Genetics

B.Sc. İstanbul Technical University-Molecular Biology and Genetics

Emine Sıla Özdemir

PhD candidate in Chemical and Biological Engineering
Research
Unraveling the Molecular Mechanism of Cdc42 and Rac1 Interactions with IQGAP2

IQGAP2 is a scaffold protein which plays central roles in cell-cell adhesion, polarity and cell motility. Rho GTPases Cdc42 and Rac1, in their GTP-bound active forms, interact with all three human IQGAP isoforms. IQGAP-Cdc42 interaction promotes metastasis by enhancing actin polymerization. However, despite their high degree of sequence identity, Cdc42 and Ra1 intrections with IQGAP show differences. We aim to reveal the interaction mechanisms of these proteins.

Publications
Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2. Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R (2018) . The Journal of Biological Chemistry. doi:10.1074/jbc.RA117.001596

 

Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations. Ozgur B*Ozdemir ES*, Gursoy A, Keskin O (2017) Journal of Physical Chemistry B 121 (15):3686-3700.doi:10.1021/acs.jpcb.6b10401 *These authors contributed equally to the work.

Red emitting, cucurbituril-capped, pH-responsive conjugated oligomer-based nanoparticles for drug delivery and cellular imaging. Pennakalathil J, Jahja E, Ozdemir ES, Konu O, Tuncel D (2014) Biomacromolecules 15 (9):3366-3374. doi:10.1021/bm500839j

Short Bio
B.Sc. Bilkent University-Molecular Biology and Genetics

M.Sc. Bilkent University-Molecular Biology and Genetics

Ph.D. Koç University-Chemical and Biological Engineering

For more information see Sıla’s homepage

Serena Muratcıoğlu

PhD in Chemical and Biological Engineering
Research
Computational and experimental investigation of RAS homodimer and RAS-effector interactions

Ras proteins recruit and activate effectors, including Raf, that transmit receptor-initiated signals and regulates gene expression. Ras is believed to function as a monomer; however, since Raf dimerizes, it was suspected that Ras may also dimerize. Here we show that GTP-bound K-Ras4B forms stable homodimers using two interfaces.  We aim to confirm RAS dimerization in vivo and understand the effect of

 


Short Bio

Ph.D. Koç University-Chemical and Biological Engineering

B.Sc. Istanbul Technical University-Chemistry and Molecular Biology & Genetics

Efe Elbeyli

MSc in Biomedical Science and Engineering
Research
Critical Assessment of PRediction of Interactions with PRISM

Capri is community wide experiment to test protein-protein docking methods in blind predictions based on three-dimensional structures. Targets are selected from experimentally known but unpublished complex structures. Predictors can use any of the information in literature about the components for prediction.


Short Bio
B.Sc. Koç University-Molecular Biology and Genetics

M.Sc. Koç University-Biomedical Science and Engineering

 

Bilgesu Erdoğan

MSc in Biomedical Science and Engineering
Research
Mutation Mapping on Protein-Protein Interaction Networks

Diseases are commonly the result of dysregulated complex interactions involving large sets of genes and proteins as products of these genes, and their cooperation with other cellular components. Interpreting protein-protein interactions at both network and molecular interaction levels with mutation knowledge requires a comprehensive research process that is fed from different sources. In this project, we developed a web-based tool, Gene2Phen, by integrating large-scale protein-protein interaction network, 3D protein structure information and interface mutation knowledge to aid researchers in exploring and comparing the molecular mechanism of different phenotypes. Gene2Phen works as an automatized pipeline tool to build, visualize and compare phenotype specific subnetworks, to examine protein- protein interactions associated with their structure and mutation data. Gene2Phen web tool prioritizes the human protein-protein network based on seed genes specific to a phenotype. From the prioritized-PPI network, users can generate a phenotype specific subnetwork. The phenotype-specific subnetworks can be visualized and compared interactively. Genome annotations and topological properties of each protein are shown in this interactive network representation. A unique feature of Gene2Phen is its ability to display 3D structural models of protein-protein interactions and their predicted protein-protein interfaces. Users can see the list of mutations which are mapped on predicted protein-protein interfaces. This allows users to study mutations altering protein-protein interfaces and their role in the phenotype-specific subnetworks. Gene2Phen, by automating the integration of protein-protein networks, protein structure, and disease – related mutations at large scale, will not only boost the productivity and efficiency, but it may be the leveraging step to the novel solutions/studies. 

Short Bio

M.Sc. Koç University-Biomedical Science and Engineering

B.Sc. Bilkent University-Computer Engineering

Asma Hakouz

MSc in Computer Science and Engineering
Research
Physical interactions between proteins are mapped into a network called protein-protein interaction network (PPIN)  where nodes represent proteins and edges represent pairwise interactions between proteins in the network. Analysis of PPINs is important and essential to understanding biological functions and processes.  However, PPINs do not indicate structural and chemical features of interactions, therefore structural PPINs (SPPIN) should be constructed and analyzed in order to give better results and understanding of the problem. My research will focus on the analysis of SPPINs.

Short Bio

M.Sc. Koç University – Computer Science and Engineering

B.Sc. The University of Jordan – Electrical Engineering

For more information see Asma’s homepage

Meltem Eda Ömür

MSc in Molecular Biology and Genetics
Research
Updating Non-redundant Unique Interface Structures as Templates for Modeling Protein Interactions

Classification of structures of protein-protein interactions may provide valuable insights for modeling and abstracting design principles. We aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites and expand previously created interface datasets. The novelty in this work is in generating structurally non-redundant protein-protein interfaces which are sensitive to small perturbations in protein binding sites that have a significant impact in template-based docking.

Short Bio

M.Sc. Koç University-Molecular Biology and Genetics

B.Sc. Üsküdar University-Computer Engineering (Double Major)

B.Sc. Üsküdar University-Molecular Biology and Genetics

Farideh Halakou

PhD candidate in Computer Science and Engineering
Research
Efficient Algorithms for Enriching Traditional Protein-protein Interaction Networks with Proteins Alternative Conformations

The common practice in structural PPI networks is to consider just one specific conformation for each protein. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different protein interactions, functions, and downstream signaling. We propose a new representation for structural PPI networks which inspects the different conformations of proteins.

Publications
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A.  Sci Rep. 2017 Aug 3;7(1):7180.

Topological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases, Halakou F, Gursoy A., Kilic E. S. and Keskin O. 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Manchester, 2017, pp. 1-7.
doi: 10.1109/CIBCB.2017.8058539 ​

Short Bio
B.Sc. Mirdamad Institute of Higher Education-Computer Engineering

M.Sc. Kerman Graduate University of Technology-Information Technology Engineering

For more information see Farideh’s homepage

All