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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]Related articlesFree article

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

Martin J, Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF.

BMC Struct Biol. 2005 Sep 15;5:17.PMID: 16164759 [PubMed - indexed for MEDLINE]Related articlesFree article

Secondary structure assignment that accurately reflects physical and evolutionary characteristics.

Cubellis MV, Cailliez F, Lovell SC.

BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S8.PMID: 16351757 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment.

Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP.

Protein Eng. 1993 Jun;6(4):377-82.PMID: 8332595 [PubMed - indexed for MEDLINE]Related articles

SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements.

Kato H, Takahashi Y.

Comput Appl Biosci. 1997 Dec;13(6):593-600.PMID: 9475987 [PubMed - indexed for MEDLINE]Related articles

Amino acid propensities for secondary structures are influenced by the protein structural class.

Costantini S, Colonna G, Facchiano AM.

Biochem Biophys Res Commun. 2006 Apr 7;342(2):441-51. Epub 2006 Feb 8.PMID: 16487481 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 18729044 [PubMed - indexed for MEDLINE]Related articles

Knowledge-based protein secondary structure assignment.

Frishman D, Argos P.

Proteins. 1995 Dec;23(4):566-79.PMID: 8749853 [PubMed - indexed for MEDLINE]Related articles

ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.

Shi S, Chitturi B, Grishin NV.

Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W526-31. Epub 2009 May 6.PMID: 19420061 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Top-down approach in protein RDC data analysis: de novo estimation of the alignment tensor.

Chen K, Tjandra N.

J Biomol NMR. 2007 Aug;38(4):303-13. Epub 2007 Jun 26.PMID: 17593526 [PubMed - indexed for MEDLINE]Related articles

Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks.

Zhang W, Dunker AK, Zhou Y.

Proteins. 2008 Apr;71(1):61-7.PMID: 17932927 [PubMed - indexed for MEDLINE]Related articles

PROSIGN: a method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C(alpha) atoms.

Hosseini SR, Sadeghi M, Pezeshk H, Eslahchi C, Habibi M.

Comput Biol Chem. 2008 Dec;32(6):406-11. Epub 2008 Aug 6.PMID: 18789769 [PubMed - indexed for MEDLINE]Related articles

Comparison of spatial arrangements of secondary structural elements in proteins.

Mizuguchi K, Go N.

Protein Eng. 1995 Apr;8(4):353-62.PMID: 7567920 [PubMed - indexed for MEDLINE]Related articles

Connectivity independent protein-structure alignment: a hierarchical approach.

Kolbeck B, May P, Schmidt-Goenner T, Steinke T, Knapp EW.

BMC Bioinformatics. 2006 Nov 21;7:510.PMID: 17118190 [PubMed - indexed for MEDLINE]Related articlesFree article

Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures.

Duan M, Huang M, Ma C, Li L, Zhou Y.

Protein Sci. 2008 Sep;17(9):1505-12. Epub 2008 Jun 2.PMID: 18519808 [PubMed - indexed for MEDLINE]Related articlesFree article

Bridging the information gap: computational tools for intermediate resolution structure interpretation.

Jiang W, Baker ML, Ludtke SJ, Chiu W.

J Mol Biol. 2001 May 18;308(5):1033-44.PMID: 11352589 [PubMed - indexed for MEDLINE]Related articles

P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins.

Labesse G, Colloc'h N, Pothier J, Mornon JP.

Comput Appl Biosci. 1997 Jun;13(3):291-5.PMID: 9183534 [PubMed - indexed for MEDLINE]Related articles

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]Related articles

TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.

Veeramalai M, Ye Y, Godzik A.

BMC Bioinformatics. 2008 Aug 31;9:358.PMID: 18759993 [PubMed - indexed for MEDLINE]Related articlesFree article