The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done using one of several methods, inc - [Read more STRAP]
SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules. - [Read more SuperPose]
Excellent tool for comparing, colouring, annotating, mutating 3-D structures; a.k.a. Deep View; tutorial *Molecular Modeling for Beginners* is a must (listed on this page). - [Read more Swiss-PdbViewer]
Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures. - [Read more Wurst]
