321 Numerical methods in computational molecular biology

BD 140, Lecture TR 1:25-2:15PM Upson 111, Section R 2:30-3:20

Ron Elber, Upson 5148, ron@cs.cornell.edu, Phone 255-7416

Walk-in at:

Monday 10:00-12:00; Tuesday 10:00-11:00; Wednesday 9:00-10:00; Thursday 9:00-9:30

Friday 2:00-3:00

Numerical methods motivated by problems from computational molecular biology: Use of MATLAB to explore and experiment with numerical algorithms for computational molecular biology

Grades: 10% homework; 50% projects; 40% final

Textbooks:

Rudra Pratap, “Getting started with MATLAB 5”, Oxford University Press 1999

Charles F. Van Loan, “Introduction to Scientific Computing”, Prentice-Hall 2000

(*) Matlab preliminaries:

1. What is Matlab?
2. Sample of simple programs
3. Plotting in one and more dimensions
4. Writing functions

(*) Analysis of protein shapes

1. Plotting protein shapes (vectors, matrices)
2. Rotations and overlapping structures (least square fit, singular value decomposition)
3. Smoothing and interpolation (linear interpolations, cubic splines)
4. Clustering protein shapes (building RMS matrices, eigenvalue analysis, identification of families)

(*) Sequence analysis

1. Manipulation of characters in Matlab

2. Alignment of sequences with gaps

3. Dynamic programming

(*) Dynamics and initial value problems

1. Integrator: Euler method, Runga-Kutta, Verlet
2. Applications: Harmonic Oscillator, Polymer collapse

(*) Optimization

1. Steepest Descent

2. Conjugate gradient

3. Application: Refinement of a ring structure