[HTML][HTML] Advances in protein structure prediction and design
The prediction of protein three-dimensional structure from amino acid sequence has been a
grand challenge problem in computational biophysics for decades, owing to its intrinsic …
grand challenge problem in computational biophysics for decades, owing to its intrinsic …
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 …
ProtGPT2 is a deep unsupervised language model for protein design
Protein design aims to build novel proteins customized for specific purposes, thereby
holding the potential to tackle many environmental and biomedical problems. Recent …
holding the potential to tackle many environmental and biomedical problems. Recent …
Recent advances in de novo protein design: Principles, methods, and applications
X Pan, T Kortemme - Journal of Biological Chemistry, 2021 - ASBMB
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 …
Language models generalize beyond natural proteins
Learning the design patterns of proteins from sequences across evolution may have
promise toward generative protein design. However it is unknown whether language …
promise toward generative protein design. However it is unknown whether language …
De novo protein design, a retrospective
IV Korendovych, WF DeGrado - Quarterly reviews of biophysics, 2020 - cambridge.org
Proteins are molecular machines whose function depends on their ability to achieve
complex folds with precisely defined structural and dynamic properties. The rational design …
complex folds with precisely defined structural and dynamic properties. The rational design …
Protein design via deep learning
Proteins with desired functions and properties are important in fields like nanotechnology
and biomedicine. De novo protein design enables the production of previously unseen …
and biomedicine. De novo protein design enables the production of previously unseen …
De novo design of transmembrane β barrels
INTRODUCTION Despite their key biological roles, only a few proteins that fold into lipid
membranes have been designed de novo. A class of membrane proteins—transmembrane …
membranes have been designed de novo. A class of membrane proteins—transmembrane …
Opportunities and challenges in design and optimization of protein function
The field of protein design has made remarkable progress over the past decade. Historically,
the low reliability of purely structure-based design methods limited their application, but …
the low reliability of purely structure-based design methods limited their application, but …
Sparks of function by de novo protein design
Abstract Information in proteins flows from sequence to structure to function, with each step
causally driven by the preceding one. Protein design is founded on inverting this process …
causally driven by the preceding one. Protein design is founded on inverting this process …