CE (Combinatorial Extension) builds alignment between two protein structures by combinatorially combining aligned fragment pairs (AFPs), which are based on local geometry. The alignment paths are selectively extended or discarded and lead to a single global optimal alignment. Pairwise aligment can be performed via the web at http://cl.sdsc.edu/ce.html. Reference: Shindyalov IN and Bourne PE 1998, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng 11:739-47.

Dali was developed at the European Bioinformatics Institute. Dali is based on the comparison of intra-molecular distance matrices. The original Dali (Holm L and Sander C 1993, Protein structure comparison by alignment of distance matrices, J. Mol. Biol. 233:123-38) used a simulated annealing algorithm. A recent implementation, called DaliLite (Holm L and Park J, DaliLite workbench for protein structure comparison, Bioinformatics 16:566-7), used a branch-and-bound strategy. It is freely available for academic users. Dali is also available by email request or web submission at EBI. The Dali algorithm is the basis for FSSP, an automated classification of protein structures.

HOMSTRAD (Homologous Structure Alignment Database) provides manually curated structure alignments of homologous proteins. As of Feb 2004, the database contains 1032 families of homologous proteins.

K2 (a new version of KENOBI) gets a low-resolution alignment using secondary structure elements (SSE). It then extends the alignment to residue level by using genetic algorithm operators. K2 is available through the web at http://zlab.umassmed.edu/k2/. Reference: Szustakowski J and Weng Z 2002, K2: Protein structure comparison and their strucutral significance, Evolutionary Computation in Bioinformatics, Edit by G. Gogel and D. Corne, Mogan Kaufman.

SCOP (Structural Classification of Proteins) is a manual classification of protein structures in the Protein Data Bank. The hierarchy of protein structure contains four levels: class, fold, super-family and family. The SCOP database provides a comprehensive description of structural and evolutionary relationships between all proteins whose structure is available. Reference: Murzin A et al 1995, SCOP: a structural classification of protein database for the investigation of sequences and structures, J. Mol. Biol 247:536-40.