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Items: 1 to 20 of 105

1.

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.

2.

Identification of local variations within secondary structures of proteins.

Kumar P, Bansal M.

Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1077-86. doi: 10.1107/S1399004715003144.

PMID:
25945573
3.

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

Cao C, Wang G, Liu A, Xu S, Wang L, Zou S.

Int J Mol Sci. 2016 Mar 11;17(3):333. doi: 10.3390/ijms17030333.

4.
5.

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.

6.

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.

7.

PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements.

Law SM, Frank AT, Brooks CL 3rd.

J Comput Chem. 2014 Sep 15;35(24):1757-61. doi: 10.1002/jcc.23683.

8.

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
9.

Minimum message length inference of secondary structure from protein coordinate data.

Konagurthu AS, Lesk AM, Allison L.

Bioinformatics. 2012 Jun 15;28(12):i97-105. doi: 10.1093/bioinformatics/bts223.

10.

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

Shi S, Chitturi B, Grishin NV.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W526-31. doi: 10.1093/nar/gkp316.

11.
12.

Protein secondary structure classification revisited: processing DSSP information with PSSC.

Zacharias J, Knapp EW.

J Chem Inf Model. 2014 Jul 28;54(7):2166-79. doi: 10.1021/ci5000856.

PMID:
24866861
13.

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.

14.

Knowledge-based protein secondary structure assignment.

Frishman D, Argos P.

Proteins. 1995 Dec;23(4):566-79.

PMID:
8749853
15.

Piecewise linear approximation of protein structures using the principle of minimum message length.

Konagurthu AS, Allison L, Stuckey PJ, Lesk AM.

Bioinformatics. 2011 Jul 1;27(13):i43-51. doi: 10.1093/bioinformatics/btr240.

16.

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
17.

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.

18.

Searching for three-dimensional secondary structural patterns in proteins with ProSMoS.

Shi S, Zhong Y, Majumdar I, Sri Krishna S, Grishin NV.

Bioinformatics. 2007 Jun 1;23(11):1331-8.

PMID:
17384423
19.

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
20.

Compact Structure Patterns in Proteins.

Chitturi B, Shi S, Kinch LN, Grishin NV.

J Mol Biol. 2016 Oct 23;428(21):4392-4412. doi: 10.1016/j.jmb.2016.07.022.

PMID:
27498165

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