Computational Thermostabilization of an Enzyme

By A. Korkegian, M. Black, David Baker, Barry L. Stoddard. 2005

362 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. I. Samish
3. Jens Meiler
4. Andrew Leaver-Fay
5. Brian Kuhlman
6. Tanja Kortemme
7. Sagar D. Khare
8. Sarel Jacob Fleishman

In Molecular Biology

1. David Baker
2. I. Samish
3. Jens Meiler
4. Andrew Leaver-Fay
5. Tanja Kortemme
6. Brian Kuhlman
7. Jeffrey J. Gray
8. Sagar D. Khare

Citations in the corpus

• ProDCoNN: Protein design using a convolutional neural network (2019, methodology): “Significant progress in CPD has been made in the past few decades 1 such as enzymes design 2-8 and membrane protein design.”
• RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite (2011, methodology): “It allows the redesign of protein structure[1] and has been used to generate new protein folds[2], stabilize enzymes[3], generate novel enzymes[4,5], protein-protein interactions and inhibitors[6], and redesign specificities in protein-protein[7] and protein-DNA interactions[8].”
• Antibiotic resistance plasmids in wastewater treatment plants and their possible dissemination into the environment (2010, background): “The use of computational design has expanded to include the thermostabilization of enzymes (Korkegian et al., 2005) and the redesign of an enzyme active site for improved catalytic activity (Park et al.”
• High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design (2007, methodology): “been employed to stabilize proteins by computational protein design.(15,26) In order to generalize our conclusions about protein stabilization, we categorized mutations in terms of their potential contribution to inter-helical packing, inter-strand packing, and helix–strand packing.”
• Achievements and Challenges in Computational Protein Design. (2017, background): “4 The Current Decade of CPD, 2005–2014: From Enzymes to Membrane Proteins In 2005 the Stoddard and Baker labs conducted thermostabilization of the homodimeric hydrolase enzyme yeast cytosine deaminase (yCD), which converts cytosine to uracil [52].”
• Deconstruction of lignocellulosic biomass to fuels and chemicals. (2011, methodology): “Future computational approaches may utilize, for example, Rosetta for in silico screening of more thermostable mutants before producing them experimentally (142).”
• Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, background): “The practical uses of ROSETTADESIGN can be divided into five basic categories: design of novel folds (12), redesign of existing proteins (68), protein interface design (69), enzyme design (70), and prediction of fibril-forming regions in proteins (71).”
• RosettaDesign server for protein design (2006, methodology): “RosettaDesign has also been used to redesign small regions of a protein to increase protein stability or binding affinities (10,17,18).”