Structural alignment: Difference between revisions

Revision as of 02:02, 2 September 2021

Revision as of 19:17, 20 September 2021

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|volume=11

| issue=11

|pages=2606-26212606–2621

|doi=10.1110/ps.0215902

| pmc= 2373724

|doi-access=free

}}</ref> approaches the alignment problem from a different objective than almost all other methods. Rather than trying to find an alignment that maximally superimposes the largest number of residues, it seeks the subset of the structural alignment least likely to occur by chance. To do this it marks a local motif alignment with flags to indicate which residues simultaneously satisfy more stringent criteria: 1) Local structure overlap 2) regular secondary structure 3) 3D-superposition 4) same ordering in primary sequence. It converts the statistics of the number of residues with high-confidence matches and the size of the protein to compute an Expectation value for the outcome by chance. It excels at matching remote homologs, particularly structures generated by ab initio structure prediction to structure families such as SCOP, because it emphasizes extracting a statistically reliable sub alignment and not in achieving the maximal sequence alignment or maximal 3D superposition.<ref name="Malmstrom"></ref><ref name="robetta">{{cite journal

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|title=Protein structure prediction and analysis using the Robetta server

|authors=David E. Kim, Dylan Chivian, and David Baker

|issue= Web Server issue

|pages= W526–W531

|pmc= 441606

|doi-access= free

}}</ref>

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|pages=2559–2565

|doi=10.1093/bioinformatics/btp474

|pmid=19667079

|doi-access=free

}}</ref>It is often used in conjunction with these slower tools to pre-screen large data bases to extract the just the best E-value related structures for more exhaustive superposition or expensive calculations.

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|issue= 197

| doi=10.1186/1471-2105-5-197

|PMIDpmid= 15598351

|title=SCOPmap: Automated assignment of protein structures to evolutionary superfamilies

|authors=Sara Cheek, Yuan Qi, Sri Krishna, Lisa N Kinch, and Nick V Grishin

|page= 197

|pmc= 544345

|doi-access=free

}}</ref>

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|authors=Kai Wang, Ram Samudrala

|journal=Bioinformatics

|year=2005

|volume=21

|issue=13

|pages=2969–2977

|doi=10.1093/bioinformatics/bti471

|pmid=15860561

|doi-access=free

}}</ref>

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|year= 2016

|volume=84

|pages=(Suppl 1):15-19.

| doi=10.1002/prot.25005

|pmid=26857434

|pmc=5479680

|doi-access=free

}}</ref><ref name="Malmstrom"></ref><ref name="robetta"></ref> These decoys are notorious for getting local fragment motif structure correct, and forming some kernels of correct 3D tertiary structure but getting the full length tertiary structure wrong. In this twilight remote homology regime, Mammoth's e-values for the CASP<ref name="casp11"></ref> protein structure prediction evaluation have been show to be significantly more correlated with human ranking than SSAP or DALI.<ref name=Mammoth></ref> Mammoths ability to extract the multi-criteria partial overlaps with proteins of known structure and rank these with proper E-values, combined with its speed facilitates scanning vast numbers of decoy models against the PDB data base for identifying the most likely correct decoys based on their remote homology to known proteins.

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| authors=Lars Malmström Michael Riffle, Charlie EM Strauss, Dylan Chivian, Trisha N Davis, Richard Bonneau, David Baker

|year=2007

|journal=PLoSPLOS Biol

| volume=5

|issue=4

|pages= e76corresponding author1,2

|doi=10.1371/journal.pbio.0050076

| pmid=17373854

| pmc=1828141

|doi-access=free

}}</ref>

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<ref name="cech">{{cite journal|vauthors=Cech P, Svozil D, Hoksza D |year=2012|title= SETTER: web server for RNA structure comparison|journal=Nucleic Acids Research|volume= 40|issue=W1|pages=W42–W48|doi=10.1093/nar/gks560|pmid=22693209|pmc=3394248}}</ref>

<ref name="Diederichs">{{cite journal|author=Diederichs K. |year=1995|title= Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm|journal=Proteins|volume= 23|issue=2|pages=187–95|doi=10.1002/prot.340230208|pmid=8592700|s2cid=3469775|url=http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-40461}}</ref>

<ref name="fischer">{{cite journal|vauthors=Siew N, Elofsson A, Rychlewsk L, Fischer D |year=2000|title= MaxSub: an automated measure for the assessment of protein structure prediction quality|journal=Bioinformatics|volume= 16|pages=776–85|doi=10.1093/bioinformatics/16.9.776|pmid=11108700|issue=9|doi-access=free}}</ref>

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<ref name="havgaard">{{cite journal|vauthors=Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J |year=2005|title= Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%|journal=Bioinformatics|volume= 21|issue=9|pages=1815–24|doi=10.1093/bioinformatics/bti279|pmid=15657094|doi-access=free}}</ref>

<ref name="hoksza">{{cite journal|vauthors=Hoksza D, Svozil D |year=2012|title= Efficient RNA pairwise structure comparison by SETTER method|journal=Bioinformatics|volume= 28|issue=14|pages=1858–1864|doi=10.1093/bioinformatics/bts301|pmid=22611129|url=https://zenodo.org/record/890287/files/article.pdf|doi-access=free}}</ref>

<ref name="holm">{{cite journal|vauthors=Holm L, Sander C |pmid=8662544|year=1996|title=Mapping the protein universe|volume=273|issue=5275|pages=595–603|journal=Science|doi=10.1126/science.273.5275.595|s2cid=7509134}}</ref>

<ref name="kolodny">{{cite journal|vauthors=Kolodny R, Linial N |year=2004|title= Approximate protein structural alignment in polynomial time |journal=PNAS|volume= 101|issue=33|pages= 12201–12206|doi=10.1073/pnas.0404383101|pmid=15304646|pmc=514457|doi-access=free}}</ref>

<ref name="lathrop">{{cite journal|author=Lathrop RH. |year=1994|title= The protein threading problem with sequence amino acid interaction preferences is NP-complete|journal=Protein Eng|volume= 7|issue=9|pages=1059–68|doi=10.1093/protein/7.9.1059|pmid=7831276|citeseerx=10.1.1.367.9081}}</ref>

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<ref name="prlic">{{cite journal|vauthors=Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE |year=2010|title= Pre-calculated protein structure alignments at the RCSB PDB website |pmid=20937596|pages= 2983–2985|volume=26|issue=23|doi=10.1093/bioinformatics/btq572|pmc=3003546|journal=Bioinformatics}}</ref>

<ref name="skolnick">{{cite journal|vauthors=Zhang Y, Skolnick J |year=2005|title= The protein structure prediction problem could be solved using the current PDB library|journal= Proc Natl Acad Sci USA|pmid=15653774|doi=10.1073/pnas.0407152101 |volume=102|issue=4|pages=1029–34|pmc=545829|doi-access=free}}</ref>

<ref name="taylor">{{cite journal|vauthors=Taylor WR, Flores TP, Orengo CA |year=1994|title= Multiple protein structure alignment|journal=Protein Sci|volume= 3|issue=10|pages=1858–70|doi=10.1002/pro.5560031025|pmid=7849601|pmc=2142613}}</ref>

<ref name="theobald">{{cite journal|vauthors=Theobald DL, Wuttke DS |year=2006|title= Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem|journal=Proceedings of the National Academy of Sciences|volume= 103|pages=18521–18527|doi=10.1073/pnas.0508445103|issue=49|pmid=17130458|pmc=1664551|doi-access=free}}</ref>

<ref name="theobald2">{{cite journal|vauthors=Theobald DL, Wuttke DS |year=2006|journal=Bioinformatics|volume= 22|pages=2171–2172|doi=10.1093/bioinformatics/btl332|title=THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures|issue=17|pmid=16777907|pmc=2584349}}</ref>

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<ref name="ZhangTMalign">{{cite journal|vauthors=Zhang Y, Skolnick J |year=2005|journal=Nucleic Acids Research|volume= 33|pages= 2302–2309|doi=10.1093/nar/gki524|pmid=15849316|title=TM-align: A protein structure alignment algorithm based on the TM-score|issue=7|pmc=1084323}}</ref>

<ref name="ZhangTMscore">{{cite journal|vauthors=Zhang Y, Skolnick J |year=2004|journal=Proteins|volume= 57|pages= 702–710|doi=10.1002/prot.20264|pmid=15476259|title=Scoring function for automated assessment of protein structure template quality|issue=4|s2cid=7954787}}</ref>

}}

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* Bourne PE, Shindyalov IN. (2003): ''Structure Comparison and Alignment''. In: Bourne, P.E., Weissig, H. (Eds): ''Structural Bioinformatics''. Hoboken NJ: Wiley-Liss. {{ISBN|0-471-20200-2}}

* Yuan X, Bystroff C. (2004) "Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins", ''Bioinformatics''. Nov 5, 2004

* {{cite journal |vauthors=Jung J, Lee B | year = 2000 | title = Protein structure alignment using environmental profiles | journal = Protein Eng | volume = 13 | issue = 8| pages = 535–543 | doi=10.1093/protein/13.8.535| pmid = 10964982 | doi-access = free }}

* {{cite journal |vauthors=Ye Y, Godzik A | year = 2005 | title = Multiple flexible structure alignment using partial order graphs | journal = Bioinformatics | volume = 21 | issue = 10| pages = 2362–2369 | doi=10.1093/bioinformatics/bti353| pmid = 15746292 | doi-access = free }}

* {{cite journal |vauthors=Sippl M, Wiederstein M | year = 2008 | title = A note on difficult structure alignment problems | journal = Bioinformatics | volume = 24 | issue = 3| pages = 426–427 | doi=10.1093/bioinformatics/btm622| pmid = 18174182 | doi-access = free }}