Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

By Yang Zhang. 2013

115 citations recorded by the source corpus.

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I‐TASSER and QUARK for both free‐modeling (FM) and template‐based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK‐based ab initio models as probes allows the detection of distant‐homology templates which might be ignored by the traditional sequence profile‐based threading alignment algorithms. Further template assembly refinement by I‐TASSER resulted in successful folding of two medium‐sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I‐TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading‐constrained ab initio folding models can consistently improve the quality of the full‐length models as assessed by the GDT‐HA and hydrogen‐bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium‐size proteins (especially beta‐proteins) for nonhomologous targets. Further developments of sensitive fold‐recognition and ab initio folding methods are critical for solving these problems. Proteins 2014; 82(Suppl 2):175–187. © 2013 Wiley Periodicals, Inc.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12 (2017, methodology): “13,16,49 Here these data highlight again the remarkable gap that the current model ranking process remains to fill up.”
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade (2015, methodology): “19,38,39 To track the progress of the I-TASSER-based structure modeling pipelines, we presented a retrospective report of the Zhang-Server models in the last five CASP experiments.”
Assessment of Refinement of Template-Based Models in CASP11 (2016, background): “9,10 The refinement of a protein structure model is often considered to be the final step of prediction process, and has proved to be a daunting and independent problem in and of itself.”
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling (2016, methodology): “Just like CASP11, we compare the accuracy of UniCon3D with five topperforming CASP10 servers namely Zhang-Server and QUARK (Zhang, 2014), PMS (Joo et al., 2014), MUFold_CRF (Zhang et al., 2010) and BAKER-ROSETTASERVER.”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “…Yang et al., 2012) IntFOLD http://www.reading.ac.uk/bioinf/IntFOLD/ (Roche et al., 2011) I-Tasser http://zhanglab.ccmb.med.umich.edu/I-TASSER/ (Zhang, 2013) ModBase http://salilab.org/modbase/ (Pieper et al., 2011) Modeller/ModWeb http://salilab.org/modeller/ (Pieper et al., 2011; Yang et…”
Protein Structure and Function Prediction Using I-TASSER (2015, methodology): “The I-TASSER protocol (with the group name “Zhang-Server”) was ranked as the top server for automated protein structure prediction in the 7th to 11th CASP competitions (Zhang, 2007; Zhang, 2009; Xu et al., 2011; Zhang, 2014).”
Deep-learning contact-map guided protein structure prediction in CASP13 (2019, methodology): “Meanwhile, templates were identified for each domain by threading them through LOMETS, 22 where the domains were classified as “ Trivial, ” “ Easy, ” “ Hard, ” or “ Very Hard ” 23 based on the quality and number of threading alignments.”