The meaning of alignment: lessons from structural diversity. (Q33395520)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19105835%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

The meaning of alignment: lessons from structural diversity (English)

1 reference

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19 January 2020

1

1 reference

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19 January 2020

Anton Feenstra

series ordinal

2

1 reference

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19 January 2020

3

Jaap Heringa

1 reference

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19 January 2020

publication date

23 December 2008

1 reference

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19 January 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19105835%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

volume

9

1 reference

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19 January 2020

page(s)

556

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https://scigraph.springernature.com/pub.10.1186/1471-2105-9-556

19 January 2020

exact match

0 references

cites work

RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Alignment uncertainty and genomic analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Matt: local flexibility aids protein multiple structure alignment.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Recent evolutions of multiple sequence alignment algorithms

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Comparative analysis of protein structure alignments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

A new progressive-iterative algorithm for multiple structure alignment.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

A method for simultaneous alignment of multiple protein structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

PASS2: an automated database of protein alignments organised as structural superfamilies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

The Jalview Java alignment editor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Flexible structure alignment by chaining aligned fragment pairs allowing twists

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Swiss-PDB Viewer (Deep View).

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

DaliLite workbench for protein structure comparison

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

14 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

HOMSTRAD: a database of protein structure alignments for homologous families

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

CATH--a hierarchic classification of protein domain structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

The structural alignment between two proteins: is there a unique answer?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

SCOP: a structural classification of proteins database for the investigation of sequences and structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Enhanced graphic matrix analysis of nucleic acid and protein sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Protein structure alignment

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Suboptimal sequence alignment in molecular biology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

A database of protein structure families with common folding motifs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Genomics. Lining up to avoid bias.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Size-independent comparison of protein three-dimensional structures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630330

SABmark--a benchmark for sequence alignment that covers the entire known fold space

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19105835

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-9-556

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19105835%20AND%20SRC:MED&resulttype=core&format=json

journals/bmcbi/PirovanoFH08

19 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19105835%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

19105835

1 reference