Robust deep learning–based protein sequence design using ProteinMPNN
…, D Tischer, F Chan, B Koepnick, H Nguyen, A Kang… - Science, 2022 - science.org
Although deep learning has revolutionized protein structure prediction, almost all experimentally
characterized de novo protein designs have been generated using physically based …
characterized de novo protein designs have been generated using physically based …
De novo protein design by deep network hallucination
There has been considerable recent progress in protein structure prediction using deep neural
networks to predict inter-residue distances from amino acid sequences 1 , 2 – 3 . Here we …
networks to predict inter-residue distances from amino acid sequences 1 , 2 – 3 . Here we …
Generalized biomolecular modeling and design with RoseTTAFold All-Atom
…, X Li, GA Sutherland, A Hitchcock, CN Hunter, A Kang… - Science, 2024 - science.org
Deep learning methods have revolutionized protein structure prediction and design but are
currently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA) which …
currently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA) which …
De novo design of transmembrane β barrels
…, AK Bera, CM Chow, S Gerben, S Marx, A Kang… - Science, 2021 - science.org
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 β …
membranes have been designed de novo. A class of membrane proteins—transmembrane β …
[HTML][HTML] Engineering smart targeting nanovesicles and their combination with hydrogels for controlled drug delivery
K Elkhoury, P Koçak, A Kang, E Arab-Tehrany… - Pharmaceutics, 2020 - mdpi.com
Smart engineered and naturally derived nanovesicles, capable of targeting specific tissues
and cells and delivering bioactive molecules and drugs into them, are becoming important …
and cells and delivering bioactive molecules and drugs into them, are becoming important …
De novo design of small beta barrel proteins
…, L Carter, L Milles, H Nguyen, A Kang… - Proceedings of the …, 2023 - National Acad Sciences
Small beta barrel proteins are attractive targets for computational design because of their
considerable functional diversity despite their very small size (<70 amino acids). However, …
considerable functional diversity despite their very small size (<70 amino acids). However, …
Accurate computational design of three-dimensional protein crystals
Protein crystallization plays a central role in structural biology. Despite this, the process of
crystallization remains poorly understood and highly empirical, with crystal contacts, lattice …
crystallization remains poorly understood and highly empirical, with crystal contacts, lattice …
[HTML][HTML] De novo design of high-affinity binders of bioactive helical peptides
…, MJ MacCoss, M Expòsit, GR Lee, AK Bera, A Kang… - Nature, 2024 - nature.com
Many peptide hormones form an α-helix on binding their receptors 1 , 2 , 3 – 4 , and sensitive
methods for their detection could contribute to better clinical management of disease 5 . De …
methods for their detection could contribute to better clinical management of disease 5 . De …
Reconfigurable asymmetric protein assemblies through implicit negative design
…, BJR Timmermans, J Decarreau, HM Morris, A Kang… - Science, 2022 - science.org
Asymmetric multiprotein complexes that undergo subunit exchange play central roles in
biology but present a challenge for design because the components must not only contain …
biology but present a challenge for design because the components must not only contain …
Computational design of a synthetic PD-1 agonist
…, L Carter, I Goreshnik, A Kang… - Proceedings of the …, 2021 - National Acad Sciences
Programmed cell death protein-1 (PD-1) expressed on activated T cells inhibits T cell function
and proliferation to prevent an excessive immune response, and disease can result if this …
and proliferation to prevent an excessive immune response, and disease can result if this …