Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native…
By Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou. 2011
321 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology
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In Computational Theory and Mathematics
- Yang Zhang
- David Baker
- Robin Pearce
- Liam J. McGuffin
- Daniel B. Roche
- Jianlin Cheng
- Sergey Ovchinnikov
- Taeho C. Jo
In Materials Chemistry
- Yang Zhang
- David Baker
- Jinbo Xu
- Robin Pearce
- Sergey Ovchinnikov
- Hahnbeom Park
- David E. Kim
- Frank DiMaio
In Molecular Biology
- Yang Zhang
- Jinbo Xu
- David Baker
- Robin Pearce
- Sergey Ovchinnikov
- Sheng Wang
- Jianlin Cheng
- Hahnbeom Park
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”
- Large-scale determination of previously unsolved protein structures using evolutionary information (2015, methodology): “This approach is not very effective for the families identified as described above; for only 4 of the 122 families with HHsearch E-values greater than 1E-04 did one of the top ten hits from HHsearch or SPARKS-X match the predicted contacts (have Rc values greater than 0.6).”
- A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “Position-Specific Statistical Potential Structure 20, 1118–1126, June 6, 2012 ª2012 Elsevier Ltd All rights reserved 1121 and Xu, 2011), Seok-server (Lee et al., 2010), Zhang-Server (Xu et al., 2011), and ZHOU-SPARKS-X (Yang et al., 2011).”
- Massively parallel determination and modeling of endonuclease substrate specificity (2014, methodology): “For the protein structure modeling, templates and alignments are first identified by HHsearch (47), SPARKS-X (48) and RaptorX (49).”
- A comprehensive review and comparison of different computational methods for protein remote homology detection (2018, methodology): “org/yueyang/server/SPARKS-X/ [41] 240 | Chen et al.”
- Improving protein fold recognition by random forest (2014, methodology): “Using the same evaluation procedure as in [5,29-32], we calculated the sensitivity by taking as predictions the top-one or the top-five template proteins ranked for each target protein by classification scores.”
- Automatic structure prediction of oligomeric assemblies using Robetta in CASP12 (2017, methodology): “In RosettaCM — as well as in this pipeline — modeling begins by using 3 sequence alignment methods (Raptor, 4 Sparks, 5 and HHpred 14 ) to identify related template structures over a wide range of sequence identities.”