Welcome to the CHEM 576: Computational Chemical Biology on Spring 2025! This note serves the purpose to help students get familiar with computational tools mentioned in the syllabus and website.
THIS NOTE is unofficial and written by TA.
- instructor: Zan Luthey-Schulten
- 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 : 164 Noyes Laboratory
- Instructors : Prof. Z. Luthey-Schulten, T. Wu
- CRN : 63281
- Term : 01/21/25 - 05/07/25
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
Every next Friday afternoon 1:00 PM after the homework is released. Homework will be published in canvas.
Homework 1: due on 2025-01-31 1:00 PM
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, Biocyc Pathway Tools)
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