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 …
The protein folding problem: the role of theory
The protein folding problem was first articulated as question of how order arose from
disorder in proteins: How did the various native structures of proteins arise from interatomic …
disorder in proteins: How did the various native structures of proteins arise from interatomic …
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 …
Design of stimulus-responsive two-state hinge proteins
In nature, proteins that switch between two conformations in response to environmental
stimuli structurally transduce biochemical information in a manner analogous to how …
stimuli structurally transduce biochemical information in a manner analogous to how …
Origins of life: The Protein Folding Problem all over again?
How did specific useful protein sequences arise from simpler molecules at the origin of life?
This seemingly needle-in-a-haystack problem has remarkably close resemblance to the old …
This seemingly needle-in-a-haystack problem has remarkably close resemblance to the old …
A generic framework for hierarchical de novo protein design
Z Harteveld, J Bonet, S Rosset… - Proceedings of the …, 2022 - National Acad Sciences
De novo protein design enables the exploration of novel sequences and structures absent
from the natural protein universe. De novo design also stands as a stringent test for our …
from the natural protein universe. De novo design also stands as a stringent test for our …
Seven amino acid types suffice to create the core fold of RNA polymerase
The extant complex proteins must have evolved from ancient short and simple ancestors.
The double-ψ β-barrel (DPBB) is one of the oldest protein folds and conserved in various …
The double-ψ β-barrel (DPBB) is one of the oldest protein folds and conserved in various …
Ab initio modelling of the structure of ToxA-like and MAX fungal effector proteins
Pathogenic fungal diseases in crops are mediated by the release of effector proteins that
facilitate infection. Characterising the structure of these fungal effectors is vital to …
facilitate infection. Characterising the structure of these fungal effectors is vital to …
Recent progress using de novo design to study protein structure, design and binding interactions
J Ferrando, LA Solomon - Life, 2021 - mdpi.com
De novo protein design is a powerful methodology used to study natural functions in an
artificial-protein context. Since its inception, it has been used to reproduce a plethora of …
artificial-protein context. Since its inception, it has been used to reproduce a plethora of …
[HTML][HTML] De novo design of a highly stable ovoid TIM barrel: Unlocking pocket shape towards functional design
E ChuAlexander, R EguchiRaphael - BioDesign Research, 2022 - spj.science.org
The ability to finely control the structure of protein folds is an important prerequisite to
functional protein design. The TIM barrel fold is an important target for these efforts as it is …
functional protein design. The TIM barrel fold is an important target for these efforts as it is …