Macromolecular modeling and design in Rosetta: recent methods and frameworks
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …
in laboratories worldwide. During two decades of development by a community of …
Recent advances in de novo protein design: Principles, methods, and applications
The computational de novo protein design is increasingly applied to address a number of
key challenges in biomedicine and biological engineering. Successes in expanding …
key challenges in biomedicine and biological engineering. Successes in expanding …
Cell-free chemoenzymatic starch synthesis from carbon dioxide
T Cai, H Sun, J Qiao, L Zhu, F Zhang, J Zhang, Z Tang… - Science, 2021 - science.org
Starches, a storage form of carbohydrates, are a major source of calories in the human diet
and a primary feedstock for bioindustry. We report a chemical-biochemical hybrid pathway …
and a primary feedstock for bioindustry. We report a chemical-biochemical hybrid pathway …
Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Easy and accurate protein structure prediction using ColabFold
Since its public release in 2021, AlphaFold2 (AF2) has made investigating biological
questions, by using predicted protein structures of single monomers or full complexes, a …
questions, by using predicted protein structures of single monomers or full complexes, a …
Protein sequence design with a learned potential
The task of protein sequence design is central to nearly all rational protein engineering
problems, and enormous effort has gone into the development of energy functions to guide …
problems, and enormous effort has gone into the development of energy functions to guide …
Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …
could provide reliable answers to questions pertaining to the structure-function relationship …
[HTML][HTML] A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
MV Shapovalov, RL Dunbrack - Structure, 2011 - cell.com
Rotamer libraries are used in protein structure determination, prediction, and design. The
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite
Macromolecular modeling and design are increasingly useful in basic research,
biotechnology, and teaching. However, the absence of a user-friendly modeling framework …
biotechnology, and teaching. However, the absence of a user-friendly modeling framework …
Role of conformational sampling in computing mutation‐induced changes in protein structure and stability
The prediction of changes in protein stability and structure resulting from single amino acid
substitutions is both a fundamental test of macromolecular modeling methodology and an …
substitutions is both a fundamental test of macromolecular modeling methodology and an …