Template‐based modeling and free modeling by I‐TASSER in CASP7

By Yang Zhang. 2007

489 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

LOMETS: A local meta-threading-server for protein structure prediction (2007, methodology): “Based on the recent CASP7 experiment, the average TM-score of the models generated by I-TASSER (‘Zhang-Server’) is 16.9% higher than that of the best template (32).”
Evaluation of residue-residue contact predictions in CASP9 (2011, background): “12,13 For example, I-TASSER, one of the most successful structure prediction servers in recent CASPs,14,15 has been recently upgraded by adding an ab initio contact prediction module, which significantly improved its performance and increased the quality of the resulting models on hard targets by 4.”
iFC2: an integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content (2010, methodology): “The three top-performing 3D-structure prediction methods in the CASP8 competition, Zhang-Server ( Zhang 2007 ), RAPTOR (Xu et al. 2003) and Pro-sp3-TASSER (Zhou et al. 2007), are compared against the iFC 2 -SSC server in”
Progress and challenges in protein structure prediction. (2008, methodology): “8 Å for the templates and models, respectively, over the same aligned regions [31 ].”
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement (2012, unknown): “However, many methods, including I-TASSER (Roy et al., 2010; Zhang, 2007), can almost always generate models with correct supersecondary structures (Ben-David et al., 2009; Jauch et al., 2007), especially in the functionally conserved regions, which provide important insight for local-structure…”
I-TASSER: a unified platform for automated protein structure and function prediction (2010, unknown): “have shown significant advantages of composite approaches in protein structure prediction, which combine various techniques such as threading, ab initio modeling and atomic-level structure refinement approache”
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model (2008, background): “…[3] reveals the power of post-treatment of models predicted by individual fold recognition methods through consensus predictions (For example, ROBETTA [4], Pmodeller6 [5], Fams-ace [6]) and/or constrained template-fragment recombination and refinement (For example, Chunk-TASSER [7], I-TASSER [8]).”
Using inferred residue contacts to distinguish between correct and incorrect protein models (2008, background): “To what extent can inter-residue contact predictions from multiple sequence alignments, information which is orthogonal to that used in most structure prediction algorithms, be used to identify those models most similar to the native protein structure?”
Protein Structure and Function Prediction Using I-TASSER (2015, methodology): “As a template-based structure and function prediction protocol, the quality of the models predicted by I-TASSER relies on the availability of template proteins in the PDB and the accuracy of threading alignments as generated by LOMETS (Wu and Zhang, 2007).”
Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10 (2013, methodology): “18 I-TASSER was previously tested in large-scale benchmark and blind tests,9,12,19,20 which demonstrates significant efficiency in refining threading template structures; the quantitative data analyses showed that in around 81% of cases the RMSD of the I-TASSER models to the native is lower than…”
I-TASSER server for protein 3D structure prediction (2008, unknown): “The detail of the I-TASSER method has been described in [15, 16 ].”
Recognizing protein substructure similarity using segmental threading. (2010, methodology): “For the restraints from MUSTER, we follow the procedure used in I-TASSER (Wu et al., 2007; Zhang, 2007); i.”