De novo design of protein structure and function with RFdiffusion
2023年7月11日 · De novo protein design seeks to generate proteins with specified structural and/or functional properties, for example, making a binding interaction with a given target 12, folding into a...
De novo protein design—From new structures to programmable …
2024年2月1日 · For several decades, approaches to computational de novo protein design used physics-based approaches and atomistic representations, grounded in structural biology principles and rules derived from naturally occurring protein structures. Now, advances in AI are leading to rapid changes in methods.
Sparks of function by de novo protein design - Nature
2024年2月15日 · We examine these advances in the broader context of classical de novo protein design and consider implications for future challenges to come, including fundamental capabilities such as sequence...
The coming of age of de novo protein design | Nature
2016年9月14日 · De novo protein design explores the full sequence space, guided by the physical principles that underlie protein folding. Computational methodology has advanced to the point that a wide range...
Recent advances in de novo protein design: Principles, methods, and ...
2021年1月1日 · We describe developments in de novo generation of designable backbone structures, optimization of sequences, design scoring functions, and the design of the function. The advances not only highlight design goals reachable now but also point to the challenges and opportunities for the future of the field.
De novo protein design, a retrospective - PubMed
2020年2月11日 · An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models.
De novo design of drug-binding proteins with predictable
2024年4月4日 · In this study, we used structural bioinformatics to drive the de novo design of a high-affinity drug-binding protein. Molecular dynamics simulations accurately captured the trend in binding affinity for the series of drugs and predicted the role of water in binding.
A generic framework for hierarchical de novo protein design
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 understanding of the underlying physical principles of protein folding and may lead to the development of proteins with unmatched functional characteristics.
Sculpting conducting nanopore size and shape through de novo protein design
2024年7月18日 · By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane β-barrel pores with different diameters and pore geometries.
De novo protein design by inversion of the... : Protein Science
De novo protein design aims to create stable, well‐folded proteins with sequences distant from those found in nature and potentially new functions. To date, de novo proteins remain challenging to design because the solution space expands exponentially with each additional amino acid in the sequence. Therefore, it is crucial to develop new ...
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