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Results: 1 to 20 of 67

1.

[Verification of the PREFAB alignment database].

Astakhova TV, Lobanov MN, Poverennaia IV, Roĭtberg MA, Iakovlev VV.

Biofizika. 2012 Mar-Apr;57(2):205-11. Russian.

PMID:
22594274
[PubMed - indexed for MEDLINE]
2.

Large-scale comparison of protein sequence alignment algorithms with structure alignments.

Sauder JM, Arthur JW, Dunbrack RL Jr.

Proteins. 2000 Jul 1;40(1):6-22.

PMID:
10813826
[PubMed - indexed for MEDLINE]
3.

Quality measures for protein alignment benchmarks.

Edgar RC.

Nucleic Acids Res. 2010 Apr;38(7):2145-53. doi: 10.1093/nar/gkp1196. Epub 2010 Jan 4.

PMID:
20047958
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Refining multiple sequence alignments with conserved core regions.

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH.

Nucleic Acids Res. 2006 May 17;34(9):2598-606. Print 2006.

PMID:
16707662
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

PISCES: a protein sequence culling server.

Wang G, Dunbrack RL Jr.

Bioinformatics. 2003 Aug 12;19(12):1589-91.

PMID:
12912846
[PubMed - indexed for MEDLINE]
Free Article
6.

Multiple sequence alignment based on profile alignment of intermediate sequences.

Lu Y, Sze SH.

J Comput Biol. 2008 Sep;15(7):767-77. doi: 10.1089/cmb.2007.0132.

PMID:
18662101
[PubMed - indexed for MEDLINE]
7.

MulPSSM: a database of multiple position-specific scoring matrices of protein domain families.

Gowri VS, Krishnadev O, Swamy CS, Srinivasan N.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D243-6.

PMID:
16381855
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Gaps in structurally similar proteins: towards improvement of multiple sequence alignment.

Wrabl JO, Grishin NV.

Proteins. 2004 Jan 1;54(1):71-87.

PMID:
14705025
[PubMed - indexed for MEDLINE]
9.

SQUARE--determining reliable regions in sequence alignments.

Tress ML, Graña O, Valencia A.

Bioinformatics. 2004 Apr 12;20(6):974-5. Epub 2004 Feb 5.

PMID:
14764569
[PubMed - indexed for MEDLINE]
Free Article
10.

SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase.

David FP, Yip YL.

BMC Bioinformatics. 2008 Sep 23;9:391. doi: 10.1186/1471-2105-9-391.

PMID:
18811932
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002
[PubMed - indexed for MEDLINE]
Free Article
12.

Sequence database search using jumping alignments.

Spang R, Rehmsmeier M, Stoye J.

Proc Int Conf Intell Syst Mol Biol. 2000;8:367-75.

PMID:
10977097
[PubMed - indexed for MEDLINE]
13.

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.

PMID:
17883866
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Normalized global alignment for protein sequences.

Peris G, Marzal A.

J Theor Biol. 2011 Dec 21;291:22-8. doi: 10.1016/j.jtbi.2011.09.017. Epub 2011 Sep 21.

PMID:
21945336
[PubMed - indexed for MEDLINE]
15.

PISCES: recent improvements to a PDB sequence culling server.

Wang G, Dunbrack RL Jr.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W94-8.

PMID:
15980589
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

Xu Q, Dunbrack RL Jr.

Bioinformatics. 2012 Nov 1;28(21):2763-72. doi: 10.1093/bioinformatics/bts533. Epub 2012 Aug 31.

PMID:
22942020
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

DNA reference alignment benchmarks based on tertiary structure of encoded proteins.

Carroll H, Beckstead W, O'Connor T, Ebbert M, Clement M, Snell Q, McClellan D.

Bioinformatics. 2007 Oct 1;23(19):2648-9. Epub 2007 Aug 8.

PMID:
17686799
[PubMed - indexed for MEDLINE]
Free Article
18.

MSAT: a multiple sequence alignment tool based on TOPS.

Ren T, Veeramalai M, Tan AC, Gilbert D.

Appl Bioinformatics. 2004;3(2-3):149-58.

PMID:
15693740
[PubMed - indexed for MEDLINE]
19.

SAD--a normalized structural alignment database: improving sequence-structure alignments.

Marsden B, Abagyan R.

Bioinformatics. 2004 Oct 12;20(15):2333-44. Epub 2004 Apr 15.

PMID:
15087320
[PubMed - indexed for MEDLINE]
Free Article
20.

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.

Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8.

PMID:
16845081
[PubMed - indexed for MEDLINE]
Free PMC Article

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