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Results: 1 to 20 of 114

1.

Structural characterization of proteins using residue environments.

Mooney SD, Liang MH, DeConde R, Altman RB.

Proteins. 2005 Dec 1;61(4):741-7.

PMID:
16245324
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Identification of similar regions of protein structures using integrated sequence and structure analysis tools.

Peters B, Moad C, Youn E, Buffington K, Heiland R, Mooney S.

BMC Struct Biol. 2006 Mar 9;6:4.

PMID:
16526955
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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]
4.

Intrinsic disorder in the Protein Data Bank.

Le Gall T, Romero PR, Cortese MS, Uversky VN, Dunker AK.

J Biomol Struct Dyn. 2007 Feb;24(4):325-42.

PMID:
17206849
[PubMed - indexed for MEDLINE]
5.

Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods.

Eisenhaber F, Imperiale F, Argos P, Frömmel C.

Proteins. 1996 Jun;25(2):157-68.

PMID:
8811732
[PubMed - indexed for MEDLINE]
6.

Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins.

Reddy BV, Li WW, Shindyalov IN, Bourne PE.

Proteins. 2001 Feb 1;42(2):148-63.

PMID:
11119639
[PubMed - indexed for MEDLINE]
7.

Predicting residue-wise contact orders in proteins by support vector regression.

Song J, Burrage K.

BMC Bioinformatics. 2006 Oct 3;7:425.

PMID:
17014735
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins.

Beck DA, Alonso DO, Inoyama D, Daggett V.

Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12259-64. doi: 10.1073/pnas.0706527105. Epub 2008 Aug 19.

PMID:
18713857
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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]
10.

ArchDB: automated protein loop classification as a tool for structural genomics.

Espadaler J, Fernandez-Fuentes N, Hermoso A, Querol E, Aviles FX, Sternberg MJ, Oliva B.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D185-8.

PMID:
14681390
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

Binkowski TA, Freeman P, Liang J.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W555-8.

PMID:
15215448
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class.

Eisenhaber F, Frömmel C, Argos P.

Proteins. 1996 Jun;25(2):169-79.

PMID:
8811733
[PubMed - indexed for MEDLINE]
13.

pdbFun: mass selection and fast comparison of annotated PDB residues.

Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W133-7.

PMID:
15980442
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins.

Wang L, Eghbalnia HR, Markley JL.

J Biomol NMR. 2007 Nov;39(3):247-57.

PMID:
17899393
[PubMed - indexed for MEDLINE]
15.

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N.

Proteins. 2005 Feb 15;58(3):610-7.

PMID:
15614759
[PubMed - indexed for MEDLINE]
16.

Functional annotation by identification of local surface similarities: a novel tool for structural genomics.

Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M.

BMC Bioinformatics. 2005 Aug 2;6:194.

PMID:
16076399
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information.

Wang K, Horst JA, Cheng G, Nickle DC, Samudrala R.

PLoS Comput Biol. 2008 Sep 26;4(9):e1000181. doi: 10.1371/journal.pcbi.1000181.

PMID:
18818722
[PubMed - indexed for MEDLINE]
Free PMC Article
18.
19.

NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment.

Pattabiraman N, Namboodiri K, Lowrey A, Gaber BP.

Protein Seq Data Anal. 1990 Oct;3(5):387-405.

PMID:
2259697
[PubMed - indexed for MEDLINE]
20.

FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB.

Wernersson R, Rapacki K, Staerfeldt HH, Sackett PW, Mølgaard A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W84-8.

PMID:
16845115
[PubMed - indexed for MEDLINE]
Free PMC Article

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