[HTML][HTML] De novo protein design—From new structures to programmable functions

T Kortemme - Cell, 2024‏ - cell.com
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 …

Protein assembly by design

J Zhu, N Avakyan, A Kakkis, AM Hoffnagle… - Chemical …, 2021‏ - ACS Publications
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 …

Abdiffuser: full-atom generation of in-vitro functioning antibodies

K Martinkus, J Ludwiczak, WC Liang… - Advances in …, 2023‏ - proceedings.neurips.cc
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 …

Tinker 8: software tools for molecular design

JA Rackers, Z Wang, C Lu, ML Laury… - Journal of chemical …, 2018‏ - ACS Publications
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 …

The coming of age of de novo protein design

PS Huang, SE Boyken, D Baker - Nature, 2016‏ - nature.com
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 …

Recent advances in de novo protein design: Principles, methods, and applications

X Pan, T Kortemme - Journal of Biological Chemistry, 2021‏ - jbc.org
The computational de novo protein design is increasingly applied to address a number of
key challenges in biomedicine and biological engineering. Successes in expanding …

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 …

Multiblock polymers: panacea or Pandora's box?

FS Bates, MA Hillmyer, TP Lodge, CM Bates… - Science, 2012‏ - science.org
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 …

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

A Leaver-Fay, M Tyka, SM Lewis, OF Lange… - Methods in …, 2011‏ - Elsevier
We have recently completed a full rearchitecturing of the Rosetta molecular modeling
program, generalizing and expanding its existing functionality. The new architecture enables …

SWISS‐MODEL and the Swiss‐Pdb Viewer: an environment for comparative protein modeling

N Guex, MC Peitsch - electrophoresis, 1997‏ - Wiley Online Library
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 …