Welcome to the CHEM 576: Computational Chemical Biology on Spring 2025! This course offers a comprehensive, hands-on introduction to computational techniques for simulating biological molecules and performing bioinformatics analyses.
- instructor: Zan Luthey-Schulten 📫email: zan at illinois.edu
- TA: Tianyu Wu 📫email: tianyu16 at illinois.edu
CHEM 576 introduces fundamental computational methods applied to chemical biology, covering a variety of topics and tools essential for understanding the dynamics and structures of biological systems.
- Lecture Time : 1:00 PM - 1:50 PM
- Days : Monday, Wednesday, and Friday (MWF)
- Location : 162 Noyes Laboratory
- Instructors : Prof. Z. Luthey-Schulten, T. Wu
- CRN : 63281
- Term : 01/21/25 - 05/07/25
- Principles of Molecular Modeling
- Molecular Dynamics and Monte Carlo Simulations
- Structure Prediction in the Context of Structural and Functional Genomics
- Assembly of Integrated Biological Systems
To enroll in this course, students should have completed:
- One semester of undergraduate biochemistry
- Statistical thermodynamics (or consent of the instructor)
ZLS on Monday 5:00 pm CLSL A552, Tianyu Wu on Thursday 4:00 pm-5:00 pm RAL 44
Friday nights.
Week1 Web Resources & Databases for Proteins, Nucleic Acids, Genomes, Subcellular Pathways and Networks: Deep Learning Neural Networks (NN), Sequence/Structure Alignment Algorithms, Visualization (UNIPROT, SWISSPROT, PDB, SCOP, CATH, NCBI, KEGG, YEASTbook, BRENDA: Smith-Waterman, STAMP, VMD/MultiSeq tutorial, Biopython)
Week 2 : Evolutionary Concepts in Bioinformatics: Comparisons of sequences and structures and structure prediction (Phylogenetic Trees, MAFFT, Blast, AlphaFold3, Foldseek)
Week 3: Force Fields for Biomolecules and an Introduction to Molecular Dynamics Simulations (Nobel Prize 2013, CHARMM, AMBER, NAMD2, MARTINI/GROMACS)
Week 4: Analyzing Molecular Dynamics Simulations: Ligand Binding, Protein Interactions ( NAMD2 and MARTINI/GROMACS tutorials, radial distribution and correlation functions)
Week 5: Simulations of Protein:RNA and Protein:DNA Complexes and their Assembly ( Ribosome biogenesis, Protein/Nucleic Interactions, Network Analysis,)
Week 6: Introduction to Systems Biology and Steady-State Analysis of Metabolic Networks (Breuer et al. elife 2019, CobraPy, ESCHER)
Week 7: Subcellular Networks for DNA Replication, Transcription, and Translation in a Minimal Cell (Stochastic gene expression, Thornburg et al. Cell 2022, Gilbert et al. FCellDevBio 2023)
Week 8: Whole Cell Kinetic Modeling and Simulations: Coupled Stochastic Gene Expression and Metabolism ( Reaction-Diffusion Master Equation (RDME), Lattice Microbes tutorials, Juypter python notebook, machine learning kinetic parameters)
Week 9: Atomistic Simulations of a Minimal Cell (NSF STC QCB tutorials MARTINI/GROMACS 2024)
Contents provided by Jan Stevens
Week 10: Machine Learning of Minimal Cell Trajectories and Selection of Class Computational Projects
Contents supported by Rong Wei in Shulei Wang's group
Presentations of Computational Projects