PubMed

Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.

Singarapu KK, Mills JL, Xiao R, Acton T, Punta M, Fischer M, Honig B, Rost B, Montelione GT, Szyperski T.

Proteins. 2009 Oct 16. [Epub ahead of print] No abstract available. PMID: 19927321 [PubMed - as supplied by publisher]Related articles

The role of DNA shape in protein-DNA recognition.

Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B.

Nature. 2009 Oct 29;461(7268):1248-53.PMID: 19865164 [PubMed - in process]Related articles

Structural relationships among proteins with different global topologies and their implications for function annotation strategies.

Petrey D, Fischer M, Honig B.

Proc Natl Acad Sci U S A. 2009 Oct 13;106(41):17377-82. Epub 2009 Sep 24.PMID: 19805138 [PubMed - indexed for MEDLINE]Related articles

Nuance in the double-helix and its role in protein-DNA recognition.

Rohs R, West SM, Liu P, Honig B.

Curr Opin Struct Biol. 2009 Apr;19(2):171-7. Epub 2009 Apr 10. Review.PMID: 19362815 [PubMed - indexed for MEDLINE]Related articlesFree article

Is protein classification necessary? Toward alternative approaches to function annotation.

Petrey D, Honig B.

Curr Opin Struct Biol. 2009 Jun;19(3):363-8. Epub 2009 Mar 5. Review.PMID: 19269161 [PubMed - indexed for MEDLINE]Related articles

Outcome of a workshop on applications of protein models in biomedical research.

Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA.

Structure. 2009 Feb 13;17(2):151-9.PMID: 19217386 [PubMed - indexed for MEDLINE]Related articlesFree article

Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus.

Rossi P, Aramini JM, Xiao R, Chen CX, Nwosu C, Owens LA, Maglaqui M, Nair R, Fischer M, Acton TB, Honig B, Rost B, Montelione GT.

Proteins. 2009 Feb 1;74(2):515-9. No abstract available. PMID: 18951393 [PubMed - indexed for MEDLINE]Related articles

Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation.

Kosloff M, Alexov E, Arshavsky VY, Honig B.

J Biol Chem. 2008 Nov 7;283(45):31197-207. Epub 2008 Sep 9.PMID: 18782760 [PubMed - indexed for MEDLINE]Related articlesFree article

Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins.

Miloushev VZ, Bahna F, Ciatto C, Ahlsen G, Honig B, Shapiro L, Palmer AG 3rd.

Structure. 2008 Aug 6;16(8):1195-205.PMID: 18682221 [PubMed - indexed for MEDLINE]Related articlesFree article

Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?

Posy S, Shapiro L, Honig B.

J Mol Biol. 2008 May 9;378(4):954-68. Epub 2008 Mar 4.PMID: 18395225 [PubMed - indexed for MEDLINE]Related articlesFree article

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials.

Zhu J, Fan H, Periole X, Honig B, Mark AE.

Proteins. 2008 Sep;72(4):1171-88.PMID: 18338384 [PubMed - indexed for MEDLINE]Related articlesFree article

Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4.

Koehnke J, Jin X, Trbovic N, Katsamba PS, Brasch J, Ahlsen G, Scheiffele P, Honig B, Palmer AG 3rd, Shapiro L.

Structure. 2008 Mar;16(3):410-21.PMID: 18334216 [PubMed - indexed for MEDLINE]Related articlesFree article

Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2.

Koehnke J, Jin X, Budreck EC, Posy S, Scheiffele P, Honig B, Shapiro L.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1873-8. Epub 2008 Feb 4.PMID: 18250328 [PubMed - indexed for MEDLINE]Related articlesFree article

Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS.

Cell. 2007 Nov 2;131(3):530-43.PMID: 17981120 [PubMed - indexed for MEDLINE]Related articlesFree article

Loop modeling: Sampling, filtering, and scoring.

Soto CS, Fasnacht M, Zhu J, Forrest L, Honig B.

Proteins. 2008 Feb 15;70(3):834-43.PMID: 17729286 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of a chloride ion binding site in Na+/Cl -dependent transporters.

Forrest LR, Tavoulari S, Zhang YW, Rudnick G, Honig B.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12761-6. Epub 2007 Jul 24.PMID: 17652169 [PubMed - indexed for MEDLINE]Related articlesFree article

Local quality assessment in homology models using statistical potentials and support vector machines.

Fasnacht M, Zhu J, Honig B.

Protein Sci. 2007 Aug;16(8):1557-68. Epub 2007 Jun 28.PMID: 17600147 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein structure space is much more than the sum of its folds.

Honig B.

Nat Struct Mol Biol. 2007 Jun;14(6):458. No abstract available. PMID: 17549077 [PubMed - indexed for MEDLINE]Related articles

Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.

Sosinsky A, Honig B, Mann RS, Califano A.

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6305-10. Epub 2007 Mar 29.PMID: 17395715 [PubMed - indexed for MEDLINE]Related articlesFree article

NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif.

Singarapu KK, Liu G, Xiao R, Bertonati C, Honig B, Montelione GT, Szyperski T.

Proteins. 2007 May 1;67(2):501-4. No abstract available. PMID: 17266124 [PubMed - indexed for MEDLINE]Related articles