Improved beta‐protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation

By Philip Bradley, David Baker. 2006

67 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. Santrupti Nerli
3. Nikolaos G. Sgourakis
4. Frank DiMaio
5. David E. Kim
6. Yang Zhang
7. Rhiju Das
8. Jeffrey J. Gray

In Molecular Biology

1. David Baker
2. Nikolaos G. Sgourakis
3. Santrupti Nerli
4. Frank DiMaio
5. Yang Zhang
6. Tanja Kortemme
7. David E. Kim
8. Rhiju Das

Citations in the corpus

• PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta (2010, unknown): “The FoldTree instructs the Pose on how to convert its internal coordinates into Cartesian coordinates (Bradley and Baker, 2006) and provides a framework for controlling how local perturbations propagate through the global structure (e.”
• Alteration of enzyme specificity by computational loop remodeling and design (2009, methodology): “Third, the polypeptide backbone of the scaffold protein is remodeled by using several techniques from structure prediction (13, 33, 34) (Fig.”
• Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins. (2016, methodology): “Rosetta incorporates multiple different iterative approaches such as resampling of β-strand pairings [4], resampling of local structures identified from initial sampling [5], identification of startingmodels”
• Structure prediction for CASP8 with all-atom refinement using Rosetta (2009, methodology): “20 Multiple rounds of the rebuild-and-refine protocol were carried out, alternating between diversification and intensification,21 the end result was a very low energy but diverse set of models which, in favorable cases, bracketed the global minimum.”
• Automatic NOESY assignment in CS-RASREC-Rosetta (2014, background): “Broken-chain fold-trees (Bradley and Baker 2006) are considered and an effective sequence separation is computed which reflects the shortest path between residue i and j of the restraint in the chosen broken-chain fold-tree (Lange and Baker 2012).”
• Resolution-adapted recombination of structural features significantly improves sampling in restraint guided structure calculation (2011, unknown): “11,14,15,21 They are often implemented on a scripting level and involve considerable manual interaction.”
• Modeling Symmetric Macromolecular Structures in Rosetta3 (2011, background): “) connections. For simplicity, we will only consider the fold tree representation for this document. A fold tree is a directed acyclic connected graph composed of peptide segments together with long-range connections”
• Chemical shift-based methods in NMR structure determination (2018, methodology): “The fold information is preserved using long-range connections, which are also added as edges in the tree [53,74].”
• De Novo Enzyme Design Using Rosetta3 (2011, background): “A special fold tree [10] is created to constrain backbone movement to the designed site, i.”