Paircoil2: improved prediction of coiled coils from sequence
By A. V. McDonnell, Taijiao Jiang, Amy E. Keating, Bonnie Berger. Bioinform., 2006
454 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/67080275c2f525632c88cf8bec8612acc6963372
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In Molecular Biology
- Johannes Söding
- Lukasz Kurgan
- Andrei N. Lupas
- Ke Chen
- Bonnie Berger
- Jinbo Xu
- Sheng Wang
- William Stafford Noble
Citations in the corpus
- The genome of the pear (Pyrus bretschneideri Rehd.) (2013, methodology): “Conserved motifs were derived from domain profiles retrieved from the PFAM, PANTHER, PRINTS, PROSITE, SMART, and SUPERFAMILY databases and from PAIRCOIL2 (McDonnell et al. 2006) to specifically detect CC domains.”
- Comparative analysis of coiled-coil prediction methods. (2006, background): “…(Berger and Singh, 1997) were built on similar concepts, but increased the amount of informational input by incorporating pairwise residue correlations into the scoring matrix (PairCoil has recently been updated to PairCoil2 (McDonnell et al., 2006) trained with a larger set of coiled-coil data.).”
- The genome of Theobroma cacao (2011, unknown): “Cacao chromosome Arabidopsis chromosome C1(1321) A1(63)-A2(85)-A3(69)-A4(116)-A5(64) C2(935) A1(89)-A2(30)-A4(61)-A5(10) C3(1018) A1(70)-A3(17)-A4(63)-A5(130) C4(837) A1(21)-A2(9)-A3(94)-A4(36)-A5(44) C5(820) A1(24)-A2(51)-A3(78)-A5(37) C6(616) A1(59)-A2(15)-A4(66)-A5(26) C7(287) A1(5)-A5(32) C8(605”
- Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone (2011, methodology): “Multicoil is based on the Paircoil algorithm [8,9], which uses a probabilistic framework to detect coiled-coil-forming segments in proteins, based on residue-pair frequencies in known coiled coils.”
- Computational prediction of secondary and supersecondary structures. (2013, methodology): “Jia et al. 2011 Random forest NA Xia et al. 2010 Support vector machine NA Zou et al. 2009 Increment of diversity + quadratic discriminant analysis NA Hu et al. 2008 Support vector machine NA BhairPred 2005 Support vector machine WS β hairpin de la Cruz et al. 2002 Neural network NA SpiriCoil 2010 H”
- A Unified Multitask Architecture for Predicting Local Protein Properties (2012, methodology): “described data set containing 776 proteins [38].”