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[HTML][HTML] De novo protein design—From new structures to programmable functions
Methods from artificial intelligence (AI) trained on large datasets of sequences and
structures can now" write" proteins with new shapes and molecular functions de novo …
structures can now" write" proteins with new shapes and molecular functions de novo …
Protein assembly by design
Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …
machines and dynamic materials, ranging from protein complexes such as photosystem II …
Abdiffuser: full-atom generation of in-vitro functioning antibodies
We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
Tinker 8: software tools for molecular design
The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …
The coming of age of de novo protein design
There are 20200 possible amino-acid sequences for a 200-residue protein, of which the
natural evolutionary process has sampled only an infinitesimal subset. De novo protein …
natural evolutionary process has sampled only an infinitesimal subset. De novo protein …
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 …
De novo protein design, a retrospective
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 …
Multiblock polymers: panacea or Pandora's box?
Advances in synthetic polymer chemistry have unleashed seemingly unlimited strategies for
producing block polymers with arbitrary numbers (n) and types (k) of unique sequences of …
producing block polymers with arbitrary numbers (n) and types (k) of unique sequences of …
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
We have recently completed a full rearchitecturing of the Rosetta molecular modeling
program, generalizing and expanding its existing functionality. The new architecture enables …
program, generalizing and expanding its existing functionality. The new architecture enables …
SWISS‐MODEL and the Swiss‐Pdb Viewer: an environment for comparative protein modeling
Comparative protein modeling is increasingly gaining interest since it is of great assistance
during the rational design of mutagenesis experiments. The availability of this method, and …
during the rational design of mutagenesis experiments. The availability of this method, and …