Protein Modeling

1

Introduction and Protein Modeling Questions (PDF)

2

Models of Proteins (PDF)

3

Discrete Conformational Search (PDF)

4

Binding and Docking (PDF)

5

Molecular Dynamics Simulation (PDF)

6

Molecular Dynamics and Electrostatics (PDF)

7

Continuum Electrostatic Modeling I (PDF)

8

Continuum Electrostatic Modeling II (PDF)

9

Electrostatic Optimization and Design (PDF)

10

Electrostatics Modeling (PDF 1) (PDF 2)

11

Statistical Mechanics (PDF)

Network Modeling

12

Statistical Mechanics (cont.) (PDF)

13

Formulating and Simulating Network Models in Biology (PDF)

14

Formulating Models (PDF)

15

Nonlinear Dynamics and Stability (PDF)

16

Steady-State Problems (PDF)

17

Parameter Fitting and Estimation (PDF)

18

Parameter Estimation; Robustness, Fragility, Control (PDF)

Image Modeling

19

2-D and 3-D Light Microscopy; Image Reconstruction (PDF)

20

Deconvolution (PDF)

21

Deconvolution II (PDF)

22

Blind Deconvolution (PDF)

23

Optical Flow (PDF)

24

High-Throughput Data and its Analysis (PDF)

25

Inference and Statistics (PDF)

26

Roundup

Problem Set 1 (PDF)

pair-dat.zip (ZIP - 2.1 MB) (The ZIP file contains: pair.dat.)
pair-small.dat (DAT - 7.8 MB)
pair-tiny.dat (DAT - 1.7 MB)

Problem Set 2 (PDF)

estatic.m (M)
moldyn.m (M)
reflect.m (M)

Problem Set 3 (PDF)

calcp.m (M)
computeReactionPotential.m (M)
estatic_svd.m (M)
gencolloc.m (M)
readpanel.m (M)
readpanels.m (M)
loadComplex.m (M)
sphere48.qif (QIF)
sphere192.qif (QIF)
sphere768.qif (QIF)

Problem Set 4 (PDF)

integrate.m (M)
lambda.m (M)
newton.m (M)

Problem Set 5 (PDF)

descent.m (M)
lambda2.m (M)

Problem Set 6 (PDF)

mandrill.bmp (BMP)
circul.m (M)
load_data.m (M)
loadWaveletBasis.m (M)
partial_inv.m (M)