New algorithms and an in silico benchmark for computational enzyme design

By A. Zanghellini, Lin Jiang, Andrew M. Wollacott, Gong Cheng, Jens Meiler, Eric A. Althoff, Daniela Röthlisberger, David Baker. Protein Science, 2006

350 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7420c1a0ecb69d5000fd6e7039124f54f91253e1

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In Molecular Biology

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

Citations in the corpus

• Alteration of enzyme specificity by computational loop remodeling and design (2009, neutral): “Second, protein side-chain functional groups important for specific interactions between the enzyme and the reaction transition state are optimally positioned in the model, analogous to the ‘‘inverse rotamers’’ described in a previous study (32).”
• Algorithms for Protein Design (2016, background): “Others, such as inverse rotamers [90], address this from a functional (i.”
• A computational method for the design of nested proteins by loop‐directed domain insertion (2018, methodology): “In order to simultaneously optimize decoys for structure and function, the matcher application 41,53 within Rosetta was also used as a filter for decoy structures after the LooDo placement algorithm and before loop closure in order to focus the structure optimization steps on Hits capable of…”
• RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite (2011, methodology): “In the Rosetta enzyme-design methodology, the active-site geometry is specified by a set of pairwise geometric constraints – called match constraints[24] – each defined between the transition-state (TS) model and a functional group from the protein (catalytic residue).”
• Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, methodology): “The R OSETTA M ATCH algorithm ( 82 ) starts from the protein backbone and attempts to build toward the specified transition state geometry.”
• Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, neutral): “…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 et al. , 2006) FixedBBProteinDesign Redesign the amino acids on a fixed protein backbone (Dantas et al. , 2003; Kortemme et al. , 2004;…”
• Emerging themes in the computational design of novel enzymes and protein–protein interfaces (2013, background): “Constellations of backbones that can support the theozyme model are searched among hundreds of small-molecule binding pockets in crystallographic protein structures [23,34].”
• Automating human intuition for protein design (2014, background): “8,9 The problem of how to alter the sequence of a naturally occurring protein to bind a new small-molecule is much more challenging, and not directly addressed by existing benchmarks.”
• Computational design of environmental sensors for the potent opioid fentanyl (2017, methodology): “For a small subset of the final 62 fentanyl binder designs, the RosettaMatch algorithm (Zanghellini et al., 2006) was used to introduce specific protein–fentanyl interactions to the subset of ketosteroid isomerase scaffold proteins (83 PDBs).”