MAT 500
Computational Genomics

(On the web at:

Protein Structure

Prof. Ray Fort
Department of Chemistry, University of Maine


"... all life on this planet contains in its genomes the record of 3.5 billion years of evolution, the lab notebooks of evolution's experiments..."

Eric Lander (interview in the Princeton Alumni Weekly, January 2008)


Protein Structure Modeling Proteins Predicting: Structure, Function, Associations
Problem Set


Useful Web Sites
Structure Databases Structure Display Software Modeling/Predicting
Protein Databank Rasmol
(Selection and Scripting)
Build a Protein
Enzyme Structures
and Classification
WebLab Viewer Lite
(Alter Structures)
Predict Protein Server
(Secondary Structure)
Peptidases Swiss PDB Viewer
(Structure Alignment, Mutation, Homology Modeling)
PsiPred Server
(Secondary Structure)
HIV Database Kinemage
(The Original)
(Secondary Structure)
PDBSum Chime
(Browser Add-in)
(Homology Modeling)
Entrez Structure PyMol
(Ray-traced graphics)
PSA Server
(Secondary Structure,
Folding Class)
Expasy (the Swiss Institute of Bioinformatics) VMD
(Display MD simulations)
DisEMBL Server
(Predict Disordered Regions)
Atlas of Enzyme Catalytic Sites Python Molecule Viewer
(part of MGL Tools)
Rosetta Server
(Complete 3-D Structure)
Protein Informatics Resource MolSoft Browser Predict Protein secondary and Tertiary Structure
Database of Evolutionary Domains
UCSF Chimera
Graphics, numerous modeling tools
Predict Function from Structure
    CAPRI - Critical Assessment of
Predicted Interactions

  Two very useful and well-written books by Arthur Lesk:

  • Introduction to Protein Architecture, Oxford University Press, 2001

  • Introduction to Bioinformatics, Oxford University Press, 2002

Both are paperbacks, costing about $40, and are supported by excellent web sites. (I'm not suggesting these as texts, just as useful things to own.)

And the classic, by Carl Branden and John Tooze:

  • Introduction to Protein Structure, Garland Press, 1999

Also in paperback, about $50. This one has an excellent discussion of proteins as genetic switches.

This page last modified 10:17 AM on Sunday September 27th, 2009.
Webmaster, Department of Chemistry, University of Maine, Orono, ME 04469