In silico studies are approaches that enable the analysis of biological, chemical and physical systems through computer-aided simulations and modeling. Today, they provide important contributions in both academic research and applied fields. From an academic perspective, in silico approaches enable the modeling of processes at the molecular level, enabling rapid hypothesis testing and the discovery of biological mechanisms. They also provide insights that can guide experimental studies, making the research process more efficient. Since these methods enable systems to be tested in a virtual environment before proceeding to laboratory experiments, they provide great savings in terms of both cost and time. In addition, the standardized and reproducible nature of computer-aided models increases data integrity and supports the reliability of research findings.
In applied fields, the contribution of in silico studies is even more evident. Especially in drug discovery and development processes, the binding potential of new compounds to target proteins, possible toxicity levels and ADME (absorption, distribution, metabolism, excretion) profiles can be predicted in advance, thus enabling more effective and targeted progress in laboratory studies. In materials science and nanotechnology, these methods allow the properties of new polymers, surface coatings or nanomaterials to be modeled in advance, helping to design production processes more efficiently. In addition, in silico methods are utilized in fields such as agriculture, food and environmental sciences to evaluate the environmental impact of pesticides or the safety of food additives. With all these aspects, in silico studies not only contribute to the deepening of scientific knowledge, but also enable the development of more sustainable, economical and rapid solutions.
In the in silico research laboratory at our university, the use of the existing licensed Schrödinger Maestro and Material Science modules, especially in combination with the powerful hardware infrastructure provided by 32 core CPU, RTX 4090 GPU, 64 GB RAM, 1 TB SSD cloud server, offers the opportunity to perform a wide range of comprehensive computational simulations with high speed and accuracy. The main in silico studies carried out in our laboratory with our current infrastructure are summarized below:
- Protein-drug interactions animation:
- Molecular docking simulation video:
- Molecular dynamics example simulation video:
Drug Design and Biomolecular Simulations (via Maestro):
- Molecular Docking (Ligand-Protein Binding): Predicting the binding affinity of new drug candidates to target proteins.
- Molecular Dynamics Simulations (MD): Studying the stability of protein-ligand complexes over time (at high speed with Desmond GPU-powered MD).
- QSAR and ADMET Predictions: Predicting biological activity, toxicity and pharmacokinetic properties of chemical compounds.
- Protein Modeling & Homology Modeling: Modeling the structure of proteins with unknown crystal structure.
- Virtual Screening: Ability to screen different drug databases for a target
- Chemical mechanisms and equilibrium calculations
- Membrane protein modeling and membrane permeability calculations
- MM-GBSA/ MM-PBSA binding free energy calculations
Materials Science Simulations (via Materials Science Suite):
- Polymer Simulations: Model mechanical, thermal and structural properties of polymers; generate amorphous structure, calculate density and diffusion.
- Crystal Structure Optimization: Energy minimization and structure optimization of metallic, ceramic or organic crystals.
- Surface & Interface Modeling: Surface interactions and adsorption studies in coating, thin film, hetero-surface systems.
- Phase Transitions & Thermodynamic Properties: Studying the behavior of structures under the influence of temperature/pressure (e.g. glass transition temperature).
- Nanomaterial Simulations: Calculation of electronic, mechanical or surface properties of structures such as carbon nanotubes, graphene, quantum dots.
- Quantum mechanical calculations
- Nanoreactor, microkinetic calculations
In the in silico research laboratory, advanced studies in many fields such as drug discovery, biomolecular systems, functional materials and nanotechnology are carried out in both academic research and master's/doctoral projects.
