These webpages have general information for how to use several computational biochemistry tools ranging from bioinformatics to comparative modelling (homology modelling) to molecular dynamics to docking.
The information contained within these pages is primarily for students taking BIOC 475/675 offered at NDSU during the Spring 2006 semester, but is also useful to those interested in learning different computational chemistry or computational biochemistry techniques and software packages.
|
Computational Biochemistry Applications
|
| |
Using THREADER |
This tutorial demonstrates the use and analysis of THREADER to locate possible templates for a comparative modelling study. |
| |
|
|
|
| |
Primary sequence analysis |
This tutorial shows how to perform various primary sequence analysis calculations on the ProtScale website. Specifically, it illustrates how to calculate the hydropathy score, the percent of buried residues, and the average flexibility for a target and its proposed template. A brief analysis of the results is provided. |
| |
|
|
|
| |
Using Jalview |
This is a quick introduction to Jalview that discusses how to visualize and evaluate a sequence alignment. Additionally, discussion is provided on how to use Jalview to create a consensus model of secondary |
| |
|
|
|
| |
Using MODELLER |
This tutorial shows how to create protein models with MODELLER. Additionally, it provides setup and analysis tips and scripts to ease the use of MODELLER. |
| |
|
|
|
| |
Using MMTSB |
A brief introduction to using MMTSB for the energy minimization of a set of proteins and extracting the values obtained for further data analysis. This presentation (provided in PDF) was originally presented at a Computational Science Journal Club meeting. |
| |
|
|
|
| |
|
|
|
| Molecular Imagery |
| |
Creating Protein Images with VMD |
An example of creating an image of Deoxy Human Hemoglobin with VMD. More examples (tutorials section) can be found at the
VMD site. |
| |
|
|
|
| |
Creating Protein Images with Chimera |
An example of creating an image of Deoxy Human Hemoglobin with Chimera.
More examples can be found at the
Chimera site. |
| |
|
|
|
| |
|
|
|