ReviewMethods in enzymology2013
Using the RosettaSurface algorithm to predict protein structure at mineral surfaces.
Review in Methods in enzymology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Biomedical applications of solid-binding peptides and proteins.Materials today. Bio · 2023Review
- Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins.Annual review of analytical chemistry (Palo Alto, Calif.) · 2021Article
- The structural role of osteocalcin in bone biomechanics and its alteration in Type-2 Diabetes.Scientific reports · 2020Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- An adaptive geometric search algorithm for macromolecular scaffold selection.Protein engineering, design & selection : PEDS · 2018Article
- Chiral switching in biomineral suprastructures induced by homochiral l-amino acid.Science advances · 2018Article
- Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell.Science advances · 2018Article
- Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate.Nature communications · 2017Article
- Nanoscale Surface Modifications of Orthopaedic Implants: State of the Art and Perspectives.The open orthopaedics journal · 2016Article
- Article
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Authors and funding
4 authors.
Funding
Abstract
Determination of protein structure on mineral surfaces is necessary to understand biomineralization processes toward better treatment of biomineralization diseases and design of novel protein-synthesized materials. To date, limited atomic-resolution data have hindered experimental structure determination for proteins on mineral surfaces. Molecular simulation represents a complementary approach. In this chapter, we review RosettaSurface, a computational structure prediction-based algorithm designed to broadly sample conformational space to identify low-energy structures. We summarize the computational approaches, the published applications, and the new releases of the code in the Rosetta 3 framework. In addition, we provide a protocol capture to demonstrate the practical steps to employ RosettaSurface. As an example, we provide input files and output data analysis for a previously unstudied mineralization protein, osteocalcin. Finally, we summarize ongoing challenges in energy function optimization and conformational searching and suggest that the fusion between experiment and calculation is the best route forward.
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Registered trials
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