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.
(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.
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.