• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5075015)   Today's Articles (211)
For: Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2004;21:951-60. [PMID: 15531603 DOI: 10.1093/bioinformatics/bti125] [Citation(s) in RCA: 1823] [Impact Index Per Article: 86.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1801
Gabaldón T, Snel B, Zimmeren FV, Hemrika W, Tabak H, Huynen MA. Origin and evolution of the peroxisomal proteome. Biol Direct 2006;1:8. [PMID: 16556314 PMCID: PMC1472686 DOI: 10.1186/1745-6150-1-8] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 03/23/2006] [Indexed: 12/25/2022]  Open
1802
Cheng J, Baldi P. A machine learning information retrieval approach to protein fold recognition. Bioinformatics 2006;22:1456-63. [PMID: 16547073 DOI: 10.1093/bioinformatics/btl102] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
1803
Becker E, Meyer V, Madaoui H, Guerois R. Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response. Bioinformatics 2006;22:1289-92. [PMID: 16522671 DOI: 10.1093/bioinformatics/btl075] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
1804
Banfield JF, Verberkmoes NC, Hettich RL, Thelen MP. Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006;9:301-33. [PMID: 16402891 DOI: 10.1089/omi.2005.9.301] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
1805
Gordon PMK, Weinel C, Jacobi C, Kämpf U, Kriventseva E, Sensen CW. Creating hierarchical models of protein families based on Expressed Sequence Tags: The “Sprockets” analysis pipeline. Anal Chim Acta 2006;564:123-32. [PMID: 17723370 DOI: 10.1016/j.aca.2006.01.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Revised: 01/18/2006] [Accepted: 01/23/2006] [Indexed: 11/23/2022]
1806
Liu J, Glazko G, Mushegian A. Protein repertoire of double-stranded DNA bacteriophages. Virus Res 2006;117:68-80. [PMID: 16490276 DOI: 10.1016/j.virusres.2006.01.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 01/11/2006] [Accepted: 01/18/2006] [Indexed: 01/21/2023]
1807
Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE. Mimivirus and the emerging concept of "giant" virus. Virus Res 2006;117:133-44. [PMID: 16469402 DOI: 10.1016/j.virusres.2006.01.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 01/06/2006] [Accepted: 01/09/2006] [Indexed: 11/15/2022]
1808
Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A. Simple fold composition and modular architecture of the nuclear pore complex. Proc Natl Acad Sci U S A 2006;103:2172-7. [PMID: 16461911 PMCID: PMC1413685 DOI: 10.1073/pnas.0506345103] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Indexed: 11/18/2022]  Open
1809
Casbon JA, Saqi MAS. On single and multiple models of protein families for the detection of remote sequence relationships. BMC Bioinformatics 2006;7:48. [PMID: 16448555 PMCID: PMC1397874 DOI: 10.1186/1471-2105-7-48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Accepted: 01/31/2006] [Indexed: 11/23/2022]  Open
1810
Suhre K. Gene and genome duplication in Acanthamoeba polyphaga Mimivirus. J Virol 2006;79:14095-101. [PMID: 16254344 PMCID: PMC1280231 DOI: 10.1128/jvi.79.22.14095-14101.2005] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
1811
Tkaczuk KL, Obarska A, Bujnicki JM. Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol 2006;6:6. [PMID: 16433904 PMCID: PMC1397878 DOI: 10.1186/1471-2148-6-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 01/24/2006] [Indexed: 11/17/2022]  Open
1812
Neugebauer H, Herrmann C, Kammer W, Schwarz G, Nordheim A, Braun V. ExbBD-dependent transport of maltodextrins through the novel MalA protein across the outer membrane of Caulobacter crescentus. J Bacteriol 2006;187:8300-11. [PMID: 16321934 PMCID: PMC1317028 DOI: 10.1128/jb.187.24.8300-8311.2005] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
1813
Ginzinger SW, Fischer J. SimShift: Identifying structural similarities from NMR chemical shifts. Bioinformatics 2005;22:460-5. [PMID: 16317071 DOI: 10.1093/bioinformatics/bti805] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
1814
Jin J, Cai Y, Yao T, Gottschalk AJ, Florens L, Swanson SK, Gutiérrez JL, Coleman MK, Workman JL, Mushegian A, Washburn MP, Conaway RC, Conaway JW. A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J Biol Chem 2005;280:41207-12. [PMID: 16230350 DOI: 10.1074/jbc.m509128200] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
1815
Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005;33:W244-8. [PMID: 15980461 PMCID: PMC1160169 DOI: 10.1093/nar/gki408] [Citation(s) in RCA: 2953] [Impact Index Per Article: 147.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
1816
Kosinski J, Feder M, Bujnicki JM. The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. BMC Bioinformatics 2005;6:172. [PMID: 16011798 PMCID: PMC1189080 DOI: 10.1186/1471-2105-6-172] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 07/12/2005] [Indexed: 01/02/2023]  Open
1817
Simossis VA, Heringa J. PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res 2005;33:W289-94. [PMID: 15980472 PMCID: PMC1160151 DOI: 10.1093/nar/gki390] [Citation(s) in RCA: 370] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Revised: 03/10/2005] [Accepted: 03/10/2005] [Indexed: 11/14/2022]  Open
1818
Chatterjee I, Richmond A, Putiri E, Shakes DC, Singson A. TheCaenorhabditis elegans spe-38gene encodes a novel four-pass integral membrane protein required for sperm function at fertilization. Development 2005;132:2795-808. [PMID: 15930110 DOI: 10.1242/dev.01868] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
1819
Tilburn J, Sánchez-Ferrero JC, Reoyo E, Arst HN, Peñalva MA. Mutational analysis of the pH signal transduction component PalC of Aspergillus nidulans supports distant similarity to BRO1 domain family members. Genetics 2005;171:393-401. [PMID: 15944343 PMCID: PMC1456523 DOI: 10.1534/genetics.105.044644] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
1820
Coles M, Djuranovic S, Söding J, Frickey T, Koretke K, Truffault V, Martin J, Lupas AN. AbrB-like Transcription Factors Assume a Swapped Hairpin Fold that Is Evolutionarily Related to Double-Psi β Barrels. Structure 2005;13:919-28. [PMID: 15939023 DOI: 10.1016/j.str.2005.03.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 03/29/2005] [Accepted: 03/29/2005] [Indexed: 11/24/2022]
1821
Watson JD, Laskowski RA, Thornton JM. Predicting protein function from sequence and structural data. Curr Opin Struct Biol 2005;15:275-84. [PMID: 15963890 DOI: 10.1016/j.sbi.2005.04.003] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 02/04/2005] [Accepted: 04/18/2005] [Indexed: 10/25/2022]
1822
Gibson A, Lewis AP, Affleck K, Aitken AJ, Meldrum E, Thompson N. hCLCA1 and mCLCA3 are secreted non-integral membrane proteins and therefore are not ion channels. J Biol Chem 2005;280:27205-12. [PMID: 15919655 DOI: 10.1074/jbc.m504654200] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
1823
Wistrand M, Sonnhammer ELL. Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics 2005;6:99. [PMID: 15831105 PMCID: PMC1097716 DOI: 10.1186/1471-2105-6-99] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 04/15/2005] [Indexed: 11/24/2022]  Open
1824
Schuster-Böckler B, Bateman A. Visualizing profile-profile alignment: pairwise HMM logos. Bioinformatics 2005;21:2912-3. [PMID: 15827079 DOI: 10.1093/bioinformatics/bti434] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
1825
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
PrevPage 37 of 37 123334353637Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA