Structural alignment: Difference between revisions

Revision as of 21:27, 6 November 2004

Revision as of 21:00, 19 November 2004

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== Packages ==

Several tools for singlepairwise and multiple structural alignments are available on the web:

* MAMMOTH ('''Ma'''tching '''M'''olecular '''M'''odels '''O'''btained from '''T'''heory): http://ub.cbm.uam.es/mammoth/mult/

'''Pairwise'''

* CE ('''C'''ombinatorial '''E'''xtension of the optimum path): http://cl.sdsc.edu/ce.html

{| border="1" cellpadding="1"

* DALI ('''D'''istance Matrix '''A'''lignment): http://www.ebi.ac.uk/dali/

|-

* HOMSTRAD ('''Hom'''ologous '''St'''ructure '''A'''lignment '''D'''atabase): http://www-cryst.bioc.cam.ac.uk/~homstrad/

! NAME

* SARF2 ('''S'''patial '''Ar'''rangement of Backbone '''F'''ragments): http://123d.ncifcrf.gov/sarf2.html

! Description || Alignment || Link || Author || Year

* SSAP ('''S'''equential '''S'''tructure '''A'''lignment '''P'''rogram): http://www.biochem.ucl.ac.uk/cgi-bin/cath/GetSsapRasmol.pl

|-

| MAMMOTH

*| MAMMOTH ('''Ma'''tching '''M'''olecular '''M'''odels '''O'''btained from '''T'''heory): || Cα || [http://ub.cbm.uam.es/mammoth/mult/ server] || AR. Ortiz || 2002

|-

| CE

*| CE ('''C'''ombinatorial '''E'''xtension of|| theCα optimum path):|| [http://cl.sdsc.edu/ce.html server] || I. Shindyalov || 2000

|-

| DALI

*| DALI ('''D'''istance Matrix '''A'''lignment): || Contact Map || [http://www.ebi.ac.uk/dali/ server] || L. Holm || 1993

|-

| VAST

| '''V'''ector '''A'''lignment '''S'''earch '''T'''ool || SS || [http://www.ncbi.nih.gov/Structure/VAST/vastsearch.html server] || S. Bryant || 1996

|-

| PrISM

| '''P'''rotein '''I'''nformatics '''S'''ystems for '''M'''odeling || SS || [http://honiglab.cpmc.columbia.edu server] || B. Honig || 2000

|-

| SSAP

*| SSAP ('''S'''equential '''S'''tructure '''A'''lignment '''P'''rogram): || SS || [http://www.biochem.ucl.ac.uk/cgi-bin/cath/GetSsapRasmol.pl server] || C. Orengo || 1989

|-

| SARF2

*| SARF2 ('''S'''patial '''ArA'''rangementrrangements of Backbone'''B'''ackbone '''F'''ragments): || SS ||[http://123d.ncifcrf.gov/sarf2.html server] || D. Fischer || 1996

|-

| KENOBI/K2

|NA|| SS || [http://zlab.bu.edu/k2/ server] || Z. Weng || 2000

|}

== See also ==