Teaching 1

Human hemoglobin protein, 1A00, downloaded from PDB Databank. The protein is responsible of transporting oxygen in blood.

Math/bcb/coms597

Text Box: Math/BCB/ComS597 Introductory Computational Structural Biology http://www.math.iastate.edu/wu/math597.html Course Description: Introduces mathematical and computational approaches to structure prediction and determination. Topics include molecular distance geometry, potential energy minimization, and molecular dynamics simulation. Specific Subjects: Geometric representation of molecular conformation, coordinate, distance, and dihedral angle spaces, structure transformation, comparison, and visualization Molecular distance geometry, singular-value decomposition of distance matrices, least-squares fit of distance data, computational complexity Potential energy minimization, local and global optimization, simulated annealing, molecular dynamics simulation. Protein folding, inverse folding, homology modeling, secondary structure prediction. Prerequisite: Multi-Variable Calculus (Math265) and Introduction to Computer Programming (ComS227) or equivalent; Numerical Analysis (Math273) and Design and Analysis of Computer Algorithms (ComS311) are pluses, but not required. Reference Books: Molecular Modeling and Simulation by Tamar Schlick, Springer-Verlag, 2002 Structural Bioinformatics, Philip Bourne and Helge Weissig, Wiley-Liss, 2003 Course Work: Class participation (10%), homework (20%), computer projects (60%), oral presentation (10%); No exams! Late homework will only receive half of the points. No late projects! Time and Place: Lecture Time: TBA, MWF, Class Room: TBA, Office Hours: TBA, MWF, Carver 370

Computational structural biology

Text Box:

The structure of alanine dipeptide.

Lecture Notes

Text Box: 1HMVp66original.pdb 1HMVp66computed.pdb Selected Papers Presentation Schedule

Computer Project 1

Computer Project 2

Computer Project 3

Homework Assignment 1

Homework Assignment 2

Homework Assignment 3

Homework Assignment 4