PDBEB Courses 2023/2024 - Bioinformatics and Computational Biology
Organized by
Center for Neuroscience and Cell Biology
Date & Time
03/01/2024 - 12/01/2024
Location
CNC, Polo I, Auditorium 2nd floor, Coimbra
Lecturers
Aim
Molecular Visualization & Pymol
- Understand molecular visualization and how PyMOL displays complex molecular structures.
- Navigate the PyMOL interface and enhance presentation skills to capture molecular representations in education and research.
Protein Homology & Modeling
- Grasp-protein homology modeling.
- Utilize SwissModel to effectively produce accurate protein models.
- Learn to evaluate model quality and its impact on research robustness.
- Extract biological insights, such as protein-protein interactions, protein binding sites, or functional effects from the structure.
Drug-Target Analysis & DataWarrior
- Automatically download and analyze experimental information on drug affinity for specific protein targets using DataWarrior.
- Analyze drug-target interactions.
- Establish a target-ligand docking protocol to predict potential drug binding modes to a protein-target.
- Execute structural-based virtual screenings to evaluate vast virtual molecule databases to identify molecules for experimental testing.
Protein Folding & Peptide Binders
- Understand attention-based models such as AlphaFold and diffusion-based models such as RFdiffusion.
- Conduct protein folding of arbitrary sequences in clouds.
- Generate likely peptide binders for a given receptor or target protein.
- Score and evaluate candidate peptides to identify the most promising binders.
Convolutional Neural Networks (CNNs)
- Grasp the fundamental theory of CNNs.
- Design, train, and test CNN architectures for the classification and segmentation of biological images.
- Employ techniques to comprehend network predictions (Explainable AI).
Network Analysis
- Define network analysis and understand its importance.
- Recognize essential network components and terms.
- Master basic network analysis techniques.
Text-Mining
- Understand the basics of text-mining.
- Explore text-mining tools and software.
- Engage in hands-on text-mining exercises and case studies.
- Reflect on ethical considerations.
Molecular Systems Biology & Kinetic Modeling
- Familiarize with core concepts of Molecular Systems Biology.
- Gain hands-on experience with kinetic modeling and system analysis of biochemical processes, including:
o Understanding the fundamentals of chemical kinetics.
o Setting up mathematical models based on ordinary differential equations.
o Implementing models in popular software applications.
o Running simulations.
o Applying systems analysis methods to explore the properties and design principles of regulatory motifs in biochemical networks.
Modeling of tissue-level processes.
- Familiarize with different strategies of modeling biological processes at cell and tissue level
o Model cell motion and metastasis formation.
o Simulate morphology and function of vascular networks in health and disease.
o Mechanical cell-cell communication: adhesion forces.
o Bioelectrical cell-cell communication: membrane potential.
o The role of fluctuations in biological systems
Program
Available here.
