Burçin Acar

Designed novel T7RNAP sequences using ProteinMPNN and generated computational sequence and structure libraries of target fusion proteins with AlphaFold2. Developed a dynamic score to assess fusion protein functionality and allostery, while curating a fusion-protein dataset for ML model training. Provided bioinformatics support, including data processing pipelines for microplate reader and NGS data

Leveraged and customized deep learning tools, including ProteinMPNN and AlphaFold2, to design optimized protein sequences and generate extensive datasets for structural modeling and analysis. Developed a computational metric to assess the functionality of designed proteins and curated a dataset for training tailor-made ML models, deploying them on a local HPC server.

Homology-modelled nanobody structures against PATZ1 and analyzed their interaction specificity using docking and elastic network models to predict wet lab results. Developed an online tool to map causality of allosteric signaling on protein structures based on ENMs and information entropy. Optimized enhanced sampling simulations (ANM-LD) on target GPCR proteins and assisted PI on grant application

Developed a computational metric to evaluate nanobody binding strength through docking, structural, and dynamical models, validating it against experimental data. Established an internal online tool to map information transfer on proteins based on structure and dynamic models, and optimized enhanced sampling simulations on GPCR protein dynamics.

Developed an enhanced sampling simulation method (ANM-LD) for difficult conformational changes of non-globular proteins, including membrane proteins. Created scripts for input/output formatting and further analysis for ANM-LD simulations, diversifying the algorithm for various structural inputs and comprehensive sampling. Performed AFM pulling and imaging experiments with data analysis, and evalua

Developed an advanced simulation method (ANM-LD) to model complex structural changes in proteins, including membrane proteins, and created scripts to streamline input/output formatting and further analysis. Expanded the ANM-LD algorithm to handle diverse data inputs and enhance sampling techniques, while also assessing various machine learning methods on a multi-protein dataset for disease-associa

Participated in the Erasmus Exchange Student program.

Grade: 3.82/4.00

Completed a Ph.D. in Biomedical Engineering with a GPA of 3.82/4.00. The thesis focused on the 'Development of a Hybrid Methodology for Investigation and Manipulation of Functional Mechanism of Biological Macromolecules with a Focus on Nonglobular Proteins'.

Grade: 7.74/10

Obtained a Master of Science in Biomolecular Sciences with a GPA of 7.74/10, supported by a Full Scholarship of the Top Master program. Thesis I focused on 'Defining Random Coil Chemical Shifts by Intrinsically Disordered Proteins' and Thesis II on 'Determining the Role of alpha-AR and Gravin in Hippocampal Synaptic Plasticity'.

Participated as a visiting student at the Abel Lab within the Department of Biology.

Grade: 3.16/4.00

Earned a Bachelor of Science in Molecular Biology and Genetics with a GPA of 3.16/4.00. The thesis explored 'Epigenetic Concepts and The Examination of Epigenetic Basis of Variations Observed During The Barley (Hordeum Vulgare L.) Tissue Culture'.

Completed an internship at the Department of Medical Microbiology.

Participated in the Erasmus Exchange Program.