Hsymdock is a great program to generate interesting, radially symmetric protein assemblies. Many viruses use complexes with radial symmetry to perform diverse functions with the same base proetin subunits
Often times, we want to compare a new DNA sequence to other, more well known DNA sequences. this is useful to predict the function of a gene, or to idenify an idividual or species. HHpred using some clever bioninformatics tricks to rank how similar two sequenes are. It then gives you a list of sequences, ranked most to least similar
Chimera is a protein and biological macromolecule viewing prgram and much much more. It is the result of 10+ years of great wprk by many different collaborators and researchers.
An all-in-one protein strcutre and analysis program that is very easy to use. Works very well on simple proteins and protein complexes. Maintains its own database of templates and protein strucutres
The protein-folding program assosciated with HHPRED template alignment tool. This program models the 3D strucutre of a protein based on the 3D strucutres of proteins with similiar amino acid sequences.