Superpose - Revision history

Christoph: /* See also */

2009-02-04T20:02:38Z

‎See also

Christoph: /* Usage */

2009-02-04T19:27:22Z

‎Usage

Christoph: /* Topics */

2009-01-21T16:33:13Z

‎Topics

Christoph at 04:09, 29 May 2008

2008-05-29T04:09:30Z

Christoph at 04:08, 29 May 2008

2008-05-29T04:08:13Z

Christoph: /* See also */

2008-05-29T04:02:48Z

‎See also

Christoph: /* Web servers */

2008-03-31T04:28:45Z

‎Web servers

Christoph: /* Sequence Identity (SI) */

2007-10-02T07:04:39Z

‎Sequence Identity (SI)

Christoph: /* Q score */

2007-08-05T02:31:34Z

‎Q score

Christoph at 02:36, 1 August 2007

2007-08-01T02:36:47Z

@@ Line 68: / Line 68: @@
 ==See also==
 ===Topics===
-*[[wikipedia:Structural alignment software]]
+*[[wikipedia:Structural alignment]]
 *[[wikipedia:Root mean square deviation (bioinformatics)]]
-*[[wikipedia:Root mean square deviation]]
+**[[wikipedia:Root mean square deviation]]
-*[[wikipedia:Root mean square fluctuation]]
+**[[wikipedia:Root mean square fluctuation]]
 *[[wikipedia:Quaternion]] &mdash; used to optimise RMSD calculations
-*[[wikipedia:Kabsch algorithm]] &mdash; an algorithm used to minimize the RMSD by first finding the best rotation<ref name=Kabsch1976>Kabsch W (1976). "A solution for the best rotation to relate two sets of vectors". ''Acta Crystallographica'' '''32''':922–923.</ref>
+*[[wikipedia:Kabsch algorithm]] &mdash; an algorithm used to minimize the RMSD by first finding the best rotation<ref name="Kabsch1976">Kabsch W (1976). "A solution for the best rotation to relate two sets of vectors". ''Acta Crystallographica'' '''32''':922–923.</ref>
 ===Web servers===
-*[http://www.ebi.ac.uk/msd-srv/ssm/ Secondary Structure Matching (SSM)] &mdash; superpose is based off of this algorithm.
+*[http://www.ebi.ac.uk/msd-srv/ssm/ Secondary Structure Matching] (SSM) &mdash; superpose is based off of this algorithm. Uses RMSD.
-*''DALI''<ref name="Holm1993">Holm L, Sander C (1993). ''J Mol Biol, 233:123-138''.</ref>
+*''DALI''<ref name="Holm1993">Holm L, Sander C (1993). ''J Mol Biol, 233:123-138''.</ref><ref name="">Holm L, Kaariainen S, Rosenstrom P, Schenkel A. (2008) Searching protein structure databases with DaliLite v.3". ''Bioinformatics, 24:2780-2781''.</ref> &mdash; distance alignment matrix method ([http://ekhidna.biocenter.helsinki.fi/dali_server/start server], [http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/download.html download])
 *''VAST''<ref name="Gibrat1996">Gibrat J-F, Madej T, Bryant SH (1996). ''Curr Opin Struct Biol, 6:377-385''.</ref>
-*combinatorial extension (CE)<ref name="Shindyalov1998">Shindyalov IN, Bourne PE (1998). ''Protein Eng, 11:739-747''.</ref>
+*[[wikipedia:Structural_alignment#Combinatorial_extension|Combinatorial Extension]] (CE)<ref name="Shindyalov1998">Shindyalov IN, Bourne PE (1998). "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path". ''Protein Eng, 11(9):739-747''. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/9796821 9796821].</ref><ref name="Jia2004">Jia Y, Dewey TG, Shindyalov IN, Bourne PE (2004). "A new scoring function and associated statistical significance for structure alignment by CE". ''J Comput Biol, 11(5):787-799''. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15700402 15700402].</ref><ref name="Pekurovsky">Pekurovsky D, Shindyalov IN, Bourne PE (2004). "A case study of high-throughput biological data processing on parallel platforms". ''Bioinformatics, 20(12):1940-1947''. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15044237 15044237].</ref><ref name="Shindyalov">Shindyalov IN, Bourne PE (2000). "An alternative view of protein fold space". ''Proteins, 38(3):247-60''. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/10713986 10713986</ref>
 *''DEJAVU''<ref name="Kleywegt1997">Kleywegt GJ, Jones TA (1997). ''Methods Enzymol, 277:525-545''.</ref>
-*[http://www.pymolwiki.org/index.php/Cealign Cealign] &mdash; plugin for [[PyMOL]]
+*[http://www.pymolwiki.org/index.php/Cealign Cealign] &mdash; plugin for [[PyMOL]] based on CE. By Shindyalov and Bourne.<ref name="Shindyalov1998"/>
 *[http://wishart.biology.ualberta.ca/SuperPose/ SuperPose] &mdash; a protein superposition server. Uses RMSD.
 ===Related===
-*''PROMOTIF'' algorithm (Hutchinson & Thornton, 1996) &mdash; aids in calculating SSEs
+*''[http://www.msi.umn.edu/software/promotif/document_2.html PROMOTIF]'' algorithm (Hutchinson & Thornton, 1996) &mdash; aids in calculating SSEs
 *''[http://www.ccp4.ac.uk/dist/html/contact.html CONTACT]'' bricking algorithm (e.g., Tadeusz Skarzynski in ''CCP4'' suite) &mdash; computes various types of contacts in protein structures.
 *''[http://www.ccp4.ac.uk/dist/html/ncont.html NCONT]'' &mdash; analyses contacts between subsets of atoms in a PDB file.
 ==References==

@@ Line 56: / Line 56: @@
 ==Usage==
-  superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ]
+  superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [foo_out.pdb]
 where <code>[-s CID1/2]</code> are optional selection strings in MMDB convention, and <code>[foo_out.pdb]</code> is optional output file.

@@ Line 68: / Line 68: @@
 ==See also==
 ===Topics===
 *[[wikipedia:Root mean square deviation (bioinformatics)]]
 *[[wikipedia:Root mean square deviation]]
@@ Line 73: / Line 74: @@
 *[[wikipedia:Quaternion]] &mdash; used to optimise RMSD calculations
 *[[wikipedia:Kabsch algorithm]] &mdash; an algorithm used to minimize the RMSD by first finding the best rotation<ref name=Kabsch1976>Kabsch W (1976). "A solution for the best rotation to relate two sets of vectors". ''Acta Crystallographica'' '''32''':922–923.</ref>
 ===Web servers===
 *[http://www.ebi.ac.uk/msd-srv/ssm/ Secondary Structure Matching (SSM)] &mdash; superpose is based off of this algorithm.

← Older revision		Revision as of 04:09, 29 May 2008
Line 100:		Line 100:

	[[Category:Ccp4]]		[[Category:Ccp4]]
		+	[[Category:Bioinformatics]]

@@ Line 54: / Line 54: @@
 <code>SI</code> <20% is a solid indication of low structural similarity.
 ==Keywords==
@@ Line 80: / Line 88: @@
 ==References==
 <small><references/></small>
 ==External links==
 *[http://www.ebi.ac.uk/msd-srv/ssm Secondary Structure Matching (SSM) web server]

@@ Line 48: / Line 48: @@
 ===Sequence Identity (SI)===
   Nm = Nalign / min(N1,N2)
-where, Nm is the normalized alignment length.
+where, <code>Nm</code> is the normalized alignment length.
 The sequence identity is defined as a fraction of identical residues in the total number of (structurally) aligned residues:
   SI = Nident / Nalign
-SI<20% is a solid indication of low structural similarity.
+<code>SI</code> <20% is a solid indication of low structural similarity.
 ==Keywords==

@@ Line 39: / Line 39: @@
 ==Scores==
 ===Q score===
- Q = Nalign**2 / {[1+(RMSD/R0)**2]*N1*N2}
+[[Image:Ssm q-score.png|center]]
-where, Nalign is the number of residues that align with each other, N1 and N2 are the input structures, and R0 is an empirical parameter (chose at 3 A) that measure the relative significance of RMSD and Nalign.
+where, <code>Nalign</code> is the number of residues that align with each other, <code>N1</code> and <code>N2</code> are the input structures, and <code>R0</code> is an empirical parameter (chose at 3 Å) that measure the relative significance of <code>RMSD</code> and <code>Nalign</code>.
-Q reaches 1 only for identical structures (Nalign = N1 = N2 and RMSD = 0), and decreases to zero with decreasing similarity (increasing RMSD or/and decreasing Nalign. Despite the fact that the Q score represents a very basic measure that does not take into account many factors related to the quality of alignment (the number of gaps and their size, sequence identity, etc.), we found that maximization of the Q score produces good results.
+<code>Q</code> reaches 1 only for identical structures (<code>Nalign = N1 = N2</code> and <code>RMSD = 0</code>), and decreases to zero with decreasing similarity (increasing <code>RMSD</code> or/and decreasing <code>Nalign</code>. Despite the fact that the Q score represents a very basic measure that does not take into account many factors related to the quality of alignment (the number of gaps and their size, sequence identity, etc.), we found that maximization of the Q score produces good results.
 The higher the Q score the "better", in general, the alignment.

@@ Line 14: / Line 14: @@
 Several approaches to protein structure alignment have been explored over the past decade. The techniques used
 include:
-*comparison of distance matrices (DALI; Holm & Sander, 1993);
+*comparison of distance matrices (''DALI'')<ref name="Holm1993">Holm L, Sander C (1993). ''J Mol Biol, 233:123-138''.</ref>;
-*analysis of differences in vector distance plots (Orengo & Taylor, 1996);
+*analysis of differences in vector distance plots<ref name="Orengo1996">Orengo CA, Taylor WR (1996). ''Methods Enzymol, 266:617-635''.</ref>;
-*minimization of the soap-bubble surface area between two protein backbones (Falicov & Cohen, 1996);
+*minimization of the soap-bubble surface area between two protein backbones<ref name="Falicov1996">Falicov A, Cohen FE (1996). ''J Mol Biol, 258:871-892''.</ref>;
-*dynamic programming on pairwise distances between the proteins' residues (Subbiah et al., 1993; Gerstein & Levitt, 1996, 1998);
+*dynamic programming on pairwise distances between the proteins' residues<ref name="Subbiah1993">Subbiah S, Laurents DV, Levitt M (1993). ''Curr Biol, 3:141-148''.</ref><ref name="Gerstein1998">Gerstein M, Levitt M (1998). ''Protein Sci, 7:445-456''.</ref><ref name="Gerstein1996">Gerstein M, Levitt M (1996). Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, pp. 59-67. Menlo Park, California: AAAI Press.</ref>;
-*secondary-structure elements (SSEs) (Singh & Brutlag, 1997);
+*secondary-structure elements (SSEs)<ref name="Singh1997">Singh AP, Brutlag DL (1997). Proceedings of the International Conference on Intelligent Systems for Molecular Biology ISMB-97, pp. 284-293. Halkidiki, Greece: AAAI Press.</ref>;
-*three-dimensional clustering (Vriend & Sander, 1991; Mizuguchi & Go, 1995);
+*three-dimensional clustering<ref name="Vriend1991">Vriend G, Sander C (1991). ''Proteins, 11:52-58''.</ref><ref name="Mizuguchi1995">Mizuguchi K, Go N (1995). ''Protein Eng, 8:353-362''.</ref>;
-*graph theory (Mitchell et al., 1990; Alexandrov, 1996; Grindley et al., 1993);
+*graph theory<ref name="Mitchell1990">Mitchell EM, Artymiuk PJ, Rice DW, Willett PJ (1990). ''Mol Biol, 212:151-166''.</ref><ref name="Alexandrov1996">Alexandrov NN (1996). ''Protein Eng, pp.727-732''.</ref><ref name="Grindley1993">Grindley HM, Artymiuk PJ, Rice DW, Willett PJ (1993). ''Mol Biol, 229:707-721''.</ref>;
-*combinatorial extension of alignment path (CE; Shindyalov & Bourne, 1998);
+*combinatorial extension of alignment path (''CE'')<ref name="Shindyalov1998">Shindyalov IN, Bourne PE (1998). ''Protein Eng, 11:739-747''.</ref>;
-*vector alignment of SSEs (VAST; Gibrat et al., 1996);
+*vector alignment of SSEs (''VAST'')<ref name="Gibrat1996">Gibrat J-F, Madej T, Bryant SH (1996). ''Curr Opin Struct Biol, 6:377-385''.</ref>;
-*depth-first recursive search on SSE (DEJAVU; Kleywegt & Jones, 1997); and
+*depth-first recursive search on SSE (''DEJAVU'')<ref name="Kleywegt1997">Kleywegt GJ, Jones TA (1997). ''Methods Enzymol, 277:525-545''.</ref>; and
-*many others (Zuker & Somorjai, 1989; Taylor & Orengo, 1989; Godzik & Skolnick, 1994; Russell & Barton, 1992; Sali & Blundell, 1990; Barakat & Dean, 1991; Leluk et al., 2003; Jung & Lee, 2000; Kato & Takahashi, 2001).
+*many others.<ref name="Zuker1989">Zuker M, Somorjai RL (1989). ''Bull Math Biol, 51:55-78''.</ref><ref name="Taylor1989">Taylor W, Orengo CJ (1989). ''Mol Biol, 208:1-22''.</ref><ref name="Godzik1994">Godzik A, Skolnick J (1994). ''Comput Appl Biosci, 10:587-596''.</ref><ref name="Russell1992">Russell RB, Barton GJ (1992). ''Proteins, 14:309-323''.</ref><ref name="Sali1990">Sali A, Blundell TJ (1990). ''Mol Biol, 212:403-428''.</ref><ref name="Barakat1991">Barakat DW, Dean PMJ (1991). ''Comput Aided Mol Des, 5:107-117''.</ref><ref name="Leluk2003">Leluk J, Konieczny L, Roterman I (2003). ''Bioinformatics, 19:117-124''.</ref><ref name="Jung2000">Jung J, Lee B (2000). ''Protein Eng, 13:535-543''.</ref><ref name="Kato2001">Kato H, Takahashi YJ (2001). ''Chem Softw, 7:161-170''.</ref>
 Most details of protein fold may be expressed in terms of just two types of SSEs, namely helices (including what type of helix) and strands.
@@ Line 33: / Line 33: @@
 *"Strict" connectivity: Matched SSEs follow the same order along their protein chains and may be separated only by an equal number of matched or unmatched SSEs in both structures.
-The decrease in structure similarity is seen as an exponential-like increase in RMSD, which has also been found
+The decrease in structure similarity is seen as an exponential-like increase in RMSD, which has also been found in other studies.<ref name="Chotia1986">Chotia C, Lesk AM (1986). ''EMBO J, 5:823-826''.</ref><ref name="Hubbard1987">Hubbard TJP, Blundell TL (1987). ''Protein Eng, 1:159-171''.</ref><ref name="Flores1993">Flores TP, Orengo CA, Moss DC, Thornton JM (1993). ''Protein Sci, 2:1811-1826''.</ref><ref name="Russell1994">Russell RB, Barton GJ (1994). ''J Mol Biol, 244:332-350''.</ref>
-in other studies (Chotia & Lesk, 1986; Hubbard & Blundell, 1987; Flores et al., 1993; Russell & Barton, 1994; Russell et al., 1997).
 ==Keywords==
-secondary-structure elements (SSEs), singular value decomposition (SVM; of the correlation matrix, following the method described by Lesk, 1986), [[RMSD]]
+secondary-structure elements (SSEs), singular value decomposition (SVM; of the correlation matrix, following the method described by Lesk<ref name="Lesk">Lesk AM (1986). ''Acta Cryst A42, 110-113''.</ref>), [[RMSD]]
 ==See also==
 ===Web servers===
-*''DALI'' (Holm & Sander, 1993)
+*''DALI''<ref name="Holm1993">Holm L, Sander C (1993). ''J Mol Biol, 233:123-138''.</ref>
-*''VAST'' (Gibrat et al., 1996)
+*''VAST''<ref name="Gibrat1996">Gibrat J-F, Madej T, Bryant SH (1996). ''Curr Opin Struct Biol, 6:377-385''.</ref>
-*combinatorial extension (CE) (Shindyalov & Bourne, 1998)
+*combinatorial extension (CE)<ref name="Shindyalov1998">Shindyalov IN, Bourne PE (1998). ''Protein Eng, 11:739-747''.</ref>
-*''DEJAVU''
+*''DEJAVU''<ref name="Kleywegt1997">Kleywegt GJ, Jones TA (1997). ''Methods Enzymol, 277:525-545''.</ref>
 ===Related===
@@ Line 52: / Line 71: @@
 ==References==
-<references/>
+<small><references/></small>
-===Further reading===
-*Rouvray et al., 1979, and references therein &mdash; addresses the problems of structure comparison and recognition by the graph-theoretical approach.
-−
 ==External links==
 *[http://www.ebi.ac.uk/msd-srv/ssm Secondary Structure Matching (SSM) web server]