TASSER: An automated method for the prediction of protein tertiary structures in CASP6

By Yang Zhang, Adrian K. Arakaki, Jeffrey Skolnick. 2005

205 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Yang Zhang
2. Andriy Kryshtafovych
3. Krzysztof Fidelis
4. Hongyi Zhou
5. Ranjit Prasad Bahadur
6. Christopher Sander
7. Pinak Chakrabarti
8. Joël Janin

In Molecular Biology

1. Yang Zhang
2. Jinbo Xu
3. Debora Marks
4. David T. Jones
5. Christopher Sander
6. Jianlin Cheng
7. Andriy Kryshtafovych
8. Sheng Wang

Citations in the corpus

• Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “A series of ingenious methods have led to significant progress as reported in CASP since then, including threading, molecular dynamics, fragment-based assembly, contact prediction, machine learning, as well as methods combining several techniques [16,63,72,73].”
• Protein–protein interaction and quaternary structure (2008, methodology): “TASSER: an automated method for the prediction of protein tertiary structures in CASP6.”
• Ab initio protein structure prediction using chunk-TASSER. (2007, methodology): “selection, TASSER ( 33 ) full model assembly using contact potentials and distance restraints extracted from selected chunks and threading templa tes that also provide the initial starting structure, and final model selection.”
• The protein folding problem. (2008, background): “Web servers and software packages often predict the native structure of small, single-domain proteins to within about 2–6 Å of their experimental structures (8,17,242).”
• FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately (2010, background): “Recent Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments show that the most successful structure prediction methods construct their predictions from substructures that are not, in general, from proteins classified in the same fold [e.g. (3, 32, 33)].”
• Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home (2007, unknown): “In lieu of simulating full oligomeric complexes, protein structural family derived scoring functions like those pioneered by Zhang et al .,31 may complement the Rosetta all-atom physics-based terms and allow better modeling of binding interfaces, particularly for template-based problems.”
• 3D Protein Structure Predicted from Sequence (2011, unknown): “The TM scores customary in CASP reflect these differences and it is plausible that the top-­‐ranked predictions for 11 out of the 15 test proteins would be considered excellent for de novo modeled structures”
• All-atom ab initio folding of a diverse set of proteins. (2006, result): “Our results, as well as other analyses (Bradley et al., 2005; Zhang et al., 2005), suggest that the contributions of a multitude of interactions of comparable strengths rather than a single, simple dominant force may be responsible for forming protein native structure.”
• Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, background): “rithms, which are now capable of predicting certain atomic structures to angstrom accuracy.(1,2) While these algorithms work effectively for target proteins that have close homologs, predicting structures without a template or fold knowledge remains particularly challenging.”