PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
Powiadomienia systemowe
  • Sesja wygasła!
  • Sesja wygasła!
  • Sesja wygasła!
Tytuł artykułu

DomAns - pattern based method for protein domain boundaries prediction and analysis

Identyfikatory
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
Determination of the native folded structure for a particular protein is a milestone towards understanding its function, and in most cases, can be done experimentally. However, the ability to predict in silico protein structure and related features would represent a fundamental breakthough in structural biology. The ability to predict domains in proteins is amongst the most important tasks needed for efective functional classification, homology-based structure prediction, structural genomics, as it makes function prediction easier. In this paper, we present the DomAnS, protein domain prediction approach, that is based on pattern alignment. DomAnS allows rapid screening for potential domain regions with the ability to recognize the most promising regions where domains might exists. The combination of the DomAnS algorithm with specialized databases that contains all known domains, allows us to find domain regions without solving 3D structure. Our approach has been tested on CASP7 data, and for 28 targets gave the best overall score.
Rocznik
Strony
35--56
Opis fizyczny
Bibliogr. 29
Twórcy
autor
autor
autor
autor
autor
autor
  • Institute of Computing Science, Poznan University of Technology, Poznan
Bibliografia
  • [1] J. Liu, B. Rost, Sequence-based prediction of protein domains, Nucleic Acids Research 32(12) (2004) 3522-3530.
  • [2] J. Blazewicz, P. Lukasiak, M. Milostan, Some operations research methods for analyzing protein sequences and structures, 4OR: A Quarterly Journal of Operations Research 4, no. 2 (2006) 91-123.
  • [3] J. Gewehr, R. Zimmer, Ssep-domain: protein domain prediction by alignment of secondary structure elements and proJes, Bioinformatics 22(2) (2006) 181-187.
  • [4] K. Bryson, J. McGuffin, R. Marsden, J. Ward, J. Sodhi, D. Jones, Protein structure prediction servers at university college london, Nucleic Acids Research 33 (2005) W36-W38.
  • [5] R. Linding, R. Russell, V. Neduva, T. Gibson, Globplot: exploring protein sequences for globularity and disorder, Nucleic Acids Research 31 (2003) 3701-3708.
  • [6] H. Saini, D. Fischer, Meta-dp: domain prediction meta server, Bioinformatics 21(12) (2005) 29172920.
  • [7] C. Orengo, A. Michie, S. Jones, D. Jones, M. Swindells, J. Thornton, Cath-a hierarchic classification of protein domain structures, Structure 5 (1997) 1093-1108.
  • [8] F. Pearl, C. Bennett, J. Bray, A. Harrison, N. Martin, A. Shepherd, I. Sillitoe, J. Thornton, C. Orengo, The cath database: an extended protein family resource for structural and functional genomics, Nucleic Acids Research 31(1) (2003) 452-455.
  • [9] L. Holm, C. Sander, Touring protein fold space with dali/fssp, Nucleic Acids Research 26 (1998) 316-319.
  • [10] R. Finn, M. Marshall, A. Bateman, ipfam: visualization of protein-protein interactions in pdb at domain and amino acid resolutions, Bioinformatics 21 (2005) 410-412.
  • [11] A. Murzin, S. Brenner, T. Hubbard, C. Chothia, Scop: a structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology 247 (1995) 536-540.
  • [12] L. L. Conte, S. Brenner, T. Hubbard, C. Chothia, A. Murzin, Scop database in 2002: refinements accommodate structural genomics, Nucleic Acids Research 30(1) (2002) 264-267.
  • [13] A. Andreeva, D. Howorth, S. Brenner, T. Hubbard, C. Chothia, A. Murzin, Scop database in 2004: refinements integrate structure and sequence family data, Nucleic Acids Research 32 (2004) D226-D229.
  • [14] C.-H. Tai, W.-J. Lee, J. Vincent, B. Lee, Evaluation of domain prediction in casp6, PROTEINS: Structure, Function, and Bioinformatics 61 (7) (2005) 183-192.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BPP2-0019-0059
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.