Rosetta in CASP4: Progress in ab initio protein structure prediction

By Richard Bonneau, J. Tsai, Ingo Ruczinski, Dylan Chivian, Carol A. Rohl, Charles E.M. Strauss, David Baker. Proteins: Structure, Function, and Bioinformatics, 2001

316 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/25d42c89145b0c75fcd2843644ad27b33ba5b4ac

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. Yang Zhang
4. Tanja Kortemme
5. Jens Meiler
6. Roland L. Dunbrack
7. Brian Kuhlman
8. Andriy Kryshtafovych

In Molecular Biology

1. David Baker
2. Jeffrey J. Gray
3. Tanja Kortemme
4. Yang Zhang
5. Jens Meiler
6. Roland L. Dunbrack
7. Rhiju Das
8. Brian Kuhlman

Citations in the corpus

• Comparison of performance in successive CASP experiments (2001, background): “Third, Baker et al.(8) recently identified contact order as a critical variable determining predictability of fold.”
• Protein sequence design with a learned potential (2020, methodology): “We performed blind structure prediction using the AbInitio application in Rosetta [113, 114, 115] to determine whether our designed sequences could adopt structures with low RMS deviation from the starting backbone and low Rosetta energy.”
• An Integrated Framework Advancing Membrane Protein Modeling and Design (2015, methodology): “It combines Rosetta’s ab initio structure prediction protocol for soluble proteins [27] with a low-resolution score function derived from a database of structures of membrane proteins [26,28,29].”
• Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. (2003, methodology): “19 This progress has emerged through the application of the following core philosophies and techniques.”
• An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. (2003, methodology): “Next, we investigated the difference in the hydrogen bond energy of native or nativerepacked structures (native backbone coordinates with modeled side-chains from a rotamer library) and alternative conformations (decoys) generated using the ROSETTA ab initio structure prediction method.(43,44) We us”
• Local Protein Structures (2007, methodology): “It has been used with a high efficiency for improving de novo methods [317, 318].”
• CONSTANS and the CCAAT Box Binding Complex Share a Functionally Important Domain and Interact to Regulate Flowering of Arabidopsis[W][OA] (2006, methodology): “Protein Structure Predictions Protein structures were ab initio predicted using the Rosetta program (Simons et al., 1997, 1999; Bonneau et al., 2001, 2002) and the resulting pdb-files analyzed using PYMOL.”
• Development of an ab initio protein structure prediction system ABLE. (2003, unknown): “Here, as well, we compared the clustering method in [3] with our clustering method.”
• Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, unknown): “Predict the structure of a protein from its sequence (Bonneau et al. , 2001, 2002; Bradley et al. , 2005; Das et al. , 2007; Raman et al. , 2009; Simons et al. , 1997) enzdes Design a protein active site to catalyze a chemical reaction ( Jiang et al. , 2008; Rothlisberger et al. , 2008; Zanghellini…”
• Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, methodology): “evidenced by the method’s ranking among the top structure prediction groups (16, 19, 22, 28-31).”