Literature DB >> 16317077

Paircoil2: improved prediction of coiled coils from sequence.

A V McDonnell1, T Jiang, A E Keating, B Berger.   

Abstract

We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled-coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure.

Mesh:

Year:  2005        PMID: 16317077     DOI: 10.1093/bioinformatics/bti797

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  217 in total

1.  Structural dynamics and multiregion interactions in dynein-dynactin recognition.

Authors:  Jessica L Morgan; Yujuan Song; Elisar Barbar
Journal:  J Biol Chem       Date:  2011-09-19       Impact factor: 5.157

2.  Sequence TTKF ↓ QE defines the site of proteolytic cleavage in Mhp683 protein, a novel glycosaminoglycan and cilium adhesin of Mycoplasma hyopneumoniae.

Authors:  Daniel R Bogema; Nichollas E Scott; Matthew P Padula; Jessica L Tacchi; Benjamin B A Raymond; Cheryl Jenkins; Stuart J Cordwell; F Chris Minion; Mark J Walker; Steven P Djordjevic
Journal:  J Biol Chem       Date:  2011-10-03       Impact factor: 5.157

3.  Coiled coils ensure the physiological ectodomain shedding of collagen XVII.

Authors:  Wataru Nishie; Joanna Jackow; Silke C Hofmann; Claus-Werner Franzke; Leena Bruckner-Tuderman
Journal:  J Biol Chem       Date:  2012-07-03       Impact factor: 5.157

Review 4.  Metastasis: tumor cells becoming MENAcing.

Authors:  Frank Gertler; John Condeelis
Journal:  Trends Cell Biol       Date:  2010-11-09       Impact factor: 20.808

5.  Isolation and characterization of a novel v-SNARE family protein that interacts with a calcium-dependent protein kinase from the common ice plant, Mesembryanthemum crystallinum.

Authors:  E Wassim Chehab; O Rahul Patharkar; John C Cushman
Journal:  Planta       Date:  2007-03       Impact factor: 4.116

6.  Essential role of coiled coils for aggregation and activity of Q/N-rich prions and PolyQ proteins.

Authors:  Ferdinando Fiumara; Luana Fioriti; Eric R Kandel; Wayne A Hendrickson
Journal:  Cell       Date:  2010-12-23       Impact factor: 41.582

7.  Spanin function requires subunit homodimerization through intermolecular disulfide bonds.

Authors:  Joel D Berry; Manoj Rajaure; Ry Young
Journal:  Mol Microbiol       Date:  2013-02-28       Impact factor: 3.501

8.  Roles for both FtsA and the FtsBLQ subcomplex in FtsN-stimulated cell constriction in Escherichia coli.

Authors:  Bing Liu; Logan Persons; Lynda Lee; Piet A J de Boer
Journal:  Mol Microbiol       Date:  2015-01-24       Impact factor: 3.501

9.  An unpredicted aggregation-critical region of the actin-polymerizing protein TRIOBP-1/Tara, determined by elucidation of its domain structure.

Authors:  Nicholas J Bradshaw; Antony S K Yerabham; Rita Marreiros; Tao Zhang; Luitgard Nagel-Steger; Carsten Korth
Journal:  J Biol Chem       Date:  2017-04-24       Impact factor: 5.157

10.  Conformational changes in the Escherichia coli ATP synthase b-dimer upon binding to F(1)-ATPase.

Authors:  Tarek M Zaida; Tassilo Hornung; Oleg A Volkov; Andrea D Hoffman; Susan J Pandey; John G Wise; Pia D Vogel
Journal:  J Bioenerg Biomembr       Date:  2009-01-14       Impact factor: 2.945

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