RosettaDesign server for protein design

By Yi Liu, Brian Kuhlman. 2006

225 citations recorded by the source corpus.

The RosettaDesign server identifies low energy amino acid sequences for target protein structures (). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of the designed proteins. The simulations are performed using the design module of the Rosetta program (RosettaDesign). RosettaDesign uses Monte Carlo optimization with simulated annealing to search for amino acids that pack well on the target structure and satisfy hydrogen bonding potential. RosettaDesign has been experimentally validated and has been used previously to stabilize naturally occurring proteins and design a novel protein structure.

Subfields: Materials Chemistry, Molecular Biology

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

In Materials Chemistry

1. Yaoqi Zhou
2. Yuedong Yang
3. Zhixiu Li
4. Jian Zhan
5. Jeffrey J. Gray
6. Liang Dai
7. Jens Meiler
8. Alexander Derry

In Molecular Biology

1. Jeffrey J. Gray
2. Yuedong Yang
3. Yaoqi Zhou
4. Jens Meiler
5. Zhixiu Li
6. Sergey Lyskov
7. Jian Zhan
8. Namrata Anand

Citations in the corpus

• Protein sequence design with a learned potential (2022, methodology): “55,56 .”
• Protein sequence design with a learned potential (2020, methodology): “[39, 40].”
• The RosettaDock server for local protein–protein docking (2008, background): “(15) for notation] for the whole-protein complex as well as residueby-residue breakdowns and intermolecular residue-pair contributions.”
• Energy functions in de novo protein design: current challenges and future prospects. (2013, background): “The reported sequence identities range from 30% to 37% (45, 57, 66, 73, 87).”
• Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, methodology): “The R OSETTA D ESIGN server (http://rosettadesign.med.unc. edu) ( 76 ) is a Web-based interface to the fixed backbone design module of R OSETTA that allows design of proteins with up to 200 residues.”
• Algorithms for Protein Design (2016, background): “, backbone dihedral changes), a rotamer library, the energy function, and a predefined sequence space [13,43].”