SPARKS 2 and SP3 servers in CASP6

By Hongyi Zhou, Yaoqi Zhou. 2005

83 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

IntFOLD: an integrated web resource for high performance protein structure and function prediction (2019, methodology): “The IntFOLD5-TS method was newly developed for CASP13 and worked via iterative multi-template based modelling (19) using the target-template alignments from 14 alternative methods (SP3 (31), SPARKS2 (31), HHsearch (32), COMA (33), SPARKSX (34), CNFsearch (35) and the eight alternative threading meth”
Improvement of 3D protein models using multiple templates guided by single-template model quality assessment (2012, methodology): “The fold recognition methods used were SP3 and SPARKS2 (referred to hereafter as SPK2) (Zhou and Zhou, 2005), HHsearch (Soding, 2004), COMA (Soding et al., 2005) and the five alternative threading methods that are integrated into the current LOMETS (Wu and Zhang, 2007) package— QQQ, GGGd, GGGf,…”
Outcome of a workshop on archiving structural models of biological macromolecules. (2006, methodology): “…methods using the experimentally determined structures as the reference (Koh et al., 2003; Rychlewski and Fischer, 2005) and for predicting errors in a model when the actual structure is unknown (Hooft et al., 1996; Luthy et al., 1992; Melo et al., 1997; Sippl, 1995; Zhou and Zhou, 2005).”
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model (2008, background): “SPARKS, SP 3 , and SP 4 were ranked among the top performers for automatic servers in recent CASP 6 [13,14] and 7 [12,3].”
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction (2011, methodology): “The nFOLD4 algorithm, combines alignment output from in-house versions of several proﬁle-based fold recognition methods namely SP3 (9), SPARKS (9), HHsearch (10) and COMA (11), generating up to 40 alternative 3D models from bespoke 40% and 70% non-redundant template libraries.”
RaptorX: exploiting structure information for protein alignment by statistical inference (2011, methodology): “5–20 These methods have two major issues in dealing with distantly related sequence and template.”
A conditional neural fields model for protein threading (2012, methodology): “, 1998)] and several top threading methods including BThreader (Peng and Xu, 2009), Sparks (Zhou and Zhou, 2005) and MUSTER (Wu and Zhang, 2008).”
Automated tertiary structure prediction with accurate local model quality assessment using the intfold‐ts method (2011, methodology): “Two older methods, SP3 and SPARKS2,21 that were found to work well at identifying distant templates, were integrated into the pipeline.”