jV is an interactive 3D viewer program to visualize structure of protein and nucleic acid molecules. This program is also possible to use jV3 on a web browser as a Java applet.
Yorodumi is a website to easily watch, move, rotate, learn, and enjoy 3D structures of biological molecules.
Protein Globe is a graphical interface to the PDBj and other services. This service uses jV as a Java applet, so the jV available environment is required to use it.
ASH is a program to perform three-dimensional structure alignment. From the ASH homepage you can run the program over the web or download the software for free.
MAFFTash is a tool that calculates multple sequence alignments from sequences and structures.
SEALA (SEquence ALignment Analyzer) provides various tools to analyse sequence alignment.
CRNPRED is a web-based service that predicts one-dimensional protein structures including secondary structures, contact numbers, and residue-wise contact orders from amino acid sequence.
Spanner is a structural homology modeling program—that is, it threads a specific amino-acid sequence onto a specific PDB structure, patching up the gaps as best it can.
SFAS (Sequence to Function Annotation Server) is a web-based tool for predicting the structure of an amino acid sequence. SFAS runs several external programs for sequence alignment and structural modeling and organized their results. SFAS does not do any complicated calculations. There are currently several choices for alignment and one choice for structural modeling. In the future, the number of choices will be increased.
gmfit is a program for fast fitting of 3D objects using Gaussian mixture model. The fitting service between two EMDB density maps or PDB structures is available through the WEB.