Modeling structurally variable regions in homologous proteins with rosetta

By Carol A. Rohl, Charles E.M. Strauss, Dylan Chivian, David Baker. 2004

336 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. David Baker
2. Jeffrey J. Gray
3. Tanja Kortemme
4. Jens Meiler
5. Hahnbeom Park
6. Yang Zhang
7. Rhiju Das
8. David E. Kim

In Molecular Biology

1. David Baker
2. Tanja Kortemme
3. Jeffrey J. Gray
4. Jens Meiler
5. Rhiju Das
6. Po-Ssu Huang
7. Yang Zhang
8. Hahnbeom Park

Citations in the corpus

• Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “…Baker, 2009; Kaufmann et al. , 2008; Meiler and Baker, 2006) loop_modeling Predict the conformation of a set of protein loops (Mandell et al. , 2009; Rohl et al. , 2004) rna_denovo Predict the folded structure of an RNA molecule given its sequence (Das and Baker, 2007) rna_design Design a new…”
• Local Protein Structures (2007, methodology): “Rosetta method has been extended to other protein modelling problems like de novo protein design [341, 342], protein-protein docking [343], protein modelling based on limited experimental data [344, 345] and loop modelling or modelling structurally variable regions in homologous proteins [346].”
• Refinement of unreliable local regions in template‐based protein models (2012, methodology): “Following previous works,8,9 we first examined correlation of ULR G-RMSD with (i) anchor G-RMSD and (ii) initial model GDT-TS, as shown in Figure 6(a,b).”
• Protein structure prediction and analysis using the Robetta server (2004, neutral): “Unaligned regions are treated as loops, which are then modeled in the context of the fixed template using the Rosetta fragment insertion method (20).”