Physically realistic homology models built with ROSETTA can be more accurate than their templates.

By Kira M. S. Misura, Dylan Chivian, Carol A. Rohl, David E. Kim, David Baker. 2006

174 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Toward optimal fragment generations for ab initio protein structure assembly (2012, background): “11,38 For the ab initio targets, however, there are generally no long-range distance/contact predictions due to the lack of homologous global templates.”
Assessment of Contact Predictions in CASP12: Co-Evolution and Deep Learning Coming of Age (2017, positive): “7.(37,38) Fragments were obtained from the Robetta fragment server (http://www.”
Evaluation of residue-residue contact predictions in CASP9 (2011, background): “17–20 These are clearly very reliable, but their usefulness is limited to cases where templates can be identified.”
Synthetic biology - putting engineering into biology (2006, background): “However today, as an example, de novo protein structure prediction from a linear amino acids sequence can only be achieved for small protein domains at significant computational costs (Bradley, et al., 2005; Misura, et al., 2006 ).”
Assessment of protein structure refinement in CASP9 (2011, methodology): “Refinement is different from other categories in CASP and what would normally be called refinement in the literature [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] in that the refinement structures have already been refined during the TBM portion of CASP.”
Toward better refinement of comparative models: Predicting loops in inexact environments (2008, background): “Though some progress has been made, 11 – 13 both of these challenges remain unsolved in our view.”
De novo Protein Structure Prediction by Coupling Contact With Distance Profile (2020, background): “Similar to distance proﬁle, several other template-based residue-residue distance restrains are also commonly used to constrain conformation in protein structure prediction [14], [40].”
Statistical potential for assessment and prediction of protein structures (2006, methodology): “Allthe target native structures in all decoy sets were determined Wiley Bryngelson”
Evaluation of residue-residue contact prediction in CASP10 (2013, unknown): “Other studies also report that incorporating contact information into protein folding programs such as Rosetta and I-TASSER leads to improvement of the 3D models 10,11 .”
Progress and challenges in protein structure prediction. (2008, methodology): “Encouraging template refinements have been recently achieved by combining the hybrid potentials with spatial restraints from threading templates [9 ,38 ,39 ].”
Experimental accuracy in protein structure refinement via molecular dynamics simulations (2018, background): “This approach works best when the sequence similarity between the template and target is high (10), but advanced methods can generate good models when there are only distant homologs (11, 12).”
Chemical shift-based methods in NMR structure determination (2018, methodology): “Finally, the top two representatives from each cluster are used as structural templates for Rosetta’s comparative modeling protocol, RosettaCM [113,114].”
Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, methodology): “After construction of a protein backbone via de novo protein folding or comparative modeling, the model enters atom-detail refinement (15, 26, 27).”
Comparative Protein Structure Modeling Using MODELLER (2016, background): “D model for a protein that is related to at least one known protein structure (Marti-Renom et al., 2000; Fiser, 2004; Misura and Baker, 2005; Petrey and Honig, 2005; Misura et al., 2006).”