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Results: 1 to 20 of 124

1.

New enumeration algorithm for protein structure comparison and classification.

Ashby C, Johnson D, Walker K, Kanj IA, Xia G, Huang X.

BMC Genomics. 2013;14 Suppl 2:S1. doi: 10.1186/1471-2164-14-S2-S1. Epub 2013 Feb 15.

PMID:
23445440
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

SEGA: semiglobal graph alignment for structure-based protein comparison.

Mernberger M, Klebe G, H├╝llermeier E.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1330-43. doi: 10.1109/TCBB.2011.35.

PMID:
21339532
[PubMed - indexed for MEDLINE]
3.

An optimized TOPS+ comparison method for enhanced TOPS models.

Veeramalai M, Gilbert D, Valiente G.

BMC Bioinformatics. 2010 Mar 17;11:138. doi: 10.1186/1471-2105-11-138.

PMID:
20236520
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

NdPASA: a novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities.

Wang J, Feng JA.

Proteins. 2005 Feb 15;58(3):628-37.

PMID:
15616964
[PubMed - indexed for MEDLINE]
5.

Mining overrepresented 3D patterns of secondary structures in proteins.

Comin M, Guerra C, Zanotti G.

J Bioinform Comput Biol. 2008 Dec;6(6):1067-87.

PMID:
19090018
[PubMed - indexed for MEDLINE]
6.

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.

Pandit SB, Skolnick J.

BMC Bioinformatics. 2008 Dec 12;9:531. doi: 10.1186/1471-2105-9-531.

PMID:
19077267
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G.

BMC Bioinformatics. 2007 Jul 13;8:252.

PMID:
17629909
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A novel method for comparing topological models of protein structures enhanced with ligand information.

Veeramalai M, Gilbert D.

Bioinformatics. 2008 Dec 1;24(23):2698-705. doi: 10.1093/bioinformatics/btn518. Epub 2008 Oct 7.

PMID:
18842602
[PubMed - indexed for MEDLINE]
Free Article
9.

SANA: an algorithm for sequential and non-sequential protein structure alignment.

Wang L, Wu LY, Wang Y, Zhang XS, Chen L.

Amino Acids. 2010 Jul;39(2):417-25. doi: 10.1007/s00726-009-0457-y. Epub 2010 Feb 2.

PMID:
20127263
[PubMed - indexed for MEDLINE]
10.

CAALIGN: a program for pairwise and multiple protein-structure alignment.

Oldfield TJ.

Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):514-25. Epub 2007 Mar 16.

PMID:
17372357
[PubMed - indexed for MEDLINE]
11.

Angle-distance image matching techniques for protein structure comparison.

Chu CH, Tang CY, Tang CY, Pai TW.

J Mol Recognit. 2008 Nov-Dec;21(6):442-52. doi: 10.1002/jmr.914.

PMID:
18729044
[PubMed - indexed for MEDLINE]
12.

Analysis of conservation and substitutions of secondary structure elements within protein superfamilies.

Mizuguchi K, Blundell T.

Bioinformatics. 2000 Dec;16(12):1111-9.

PMID:
11159330
[PubMed - indexed for MEDLINE]
Free Article
13.

Mining super-secondary structure motifs from 3d protein structures: a sequence order independent approach.

Aung Z, Li J.

Genome Inform. 2007;19:15-26.

PMID:
18546501
[PubMed - indexed for MEDLINE]
14.

MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(╬▒) only models, Alternative alignments, and Non-sequential alignments.

Minami S, Sawada K, Chikenji G.

BMC Bioinformatics. 2013 Jan 18;14:24. doi: 10.1186/1471-2105-14-24.

PMID:
23331634
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Variable predictive model based classification algorithm for effective separation of protein structural classes.

Raghuraj R, Lakshminarayanan S.

Comput Biol Chem. 2008 Aug;32(4):302-6. doi: 10.1016/j.compbiolchem.2008.03.009. Epub 2008 Apr 1.

PMID:
18462997
[PubMed - indexed for MEDLINE]
16.

FAST: a novel protein structure alignment algorithm.

Zhu J, Weng Z.

Proteins. 2005 Feb 15;58(3):618-27.

PMID:
15609341
[PubMed - indexed for MEDLINE]
17.

An alternative view of protein fold space.

Shindyalov IN, Bourne PE.

Proteins. 2000 Feb 15;38(3):247-60.

PMID:
10713986
[PubMed - indexed for MEDLINE]
18.

Graph sharpening plus graph integration: a synergy that improves protein functional classification.

Shin H, Lisewski AM, Lichtarge O.

Bioinformatics. 2007 Dec 1;23(23):3217-24. Epub 2007 Oct 31.

PMID:
17977886
[PubMed - indexed for MEDLINE]
Free Article
19.

PALSSE: a program to delineate linear secondary structural elements from protein structures.

Majumdar I, Krishna SS, Grishin NV.

BMC Bioinformatics. 2005 Aug 11;6:202.

PMID:
16095538
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Integrated web service for improving alignment quality based on segments comparison.

Plewczynski D, Rychlewski L, Ye Y, Jaroszewski L, Godzik A.

BMC Bioinformatics. 2004 Jul 22;5:98.

PMID:
15271224
[PubMed - indexed for MEDLINE]
Free PMC Article

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