Gyu Rie Lee
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Explore the profile of Gyu Rie Lee including associated specialties, affiliations and a list of published articles.
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26
Citations
2300
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Recent Articles
1.
Anishchenko I, Kipnis Y, Kalvet I, Zhou G, Krishna R, Pellock S, et al.
bioRxiv
. 2024 Oct;
PMID: 39386615
Modeling the conformational heterogeneity of protein-small molecule systems is an outstanding challenge. We reasoned that while residue level descriptions of biomolecules are efficient for de novo structure prediction, for probing...
2.
An L, Said M, Tran L, Majumder S, Goreshnik I, Lee G, et al.
Science
. 2024 Jul;
385(6706):276-282.
PMID: 39024436
We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying...
3.
Mansoor S, Baek M, Park H, Lee G, Baker D
J Chem Theory Comput
. 2024 Mar;
20(7):2689-2695.
PMID: 38547871
Mapping the ensemble of protein conformations that contribute to function and can be targeted by small molecule drugs remains an outstanding challenge. Here, we explore the use of variational autoencoders...
4.
Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, et al.
Science
. 2024 Mar;
384(6693):eadl2528.
PMID: 38452047
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and...
5.
An L, Said M, Tran L, Majumder S, Goreshnik I, Lee G, et al.
bioRxiv
. 2024 Jan;
PMID: 38187589
A general method for designing proteins to bind and sense any small molecule of interest would be widely useful. Due to the small number of atoms to interact with, binding...
6.
Vazquez Torres S, Leung P, Venkatesh P, Lutz I, Hink F, Huynh H, et al.
Nature
. 2023 Dec;
626(7998):435-442.
PMID: 38109936
Many peptide hormones form an α-helix on binding their receptors, and sensitive methods for their detection could contribute to better clinical management of disease. De novo protein design can now...
7.
Lee G, Pellock S, Norn C, Tischer D, Dauparas J, Anischenko I, et al.
bioRxiv
. 2023 Nov;
PMID: 37961294
Despite transformative advances in protein design with deep learning, the design of small-molecule-binding proteins and sensors for arbitrary ligands remains a grand challenge. Here we combine deep learning and physics-based...
8.
Glasscock C, Pecoraro R, McHugh R, Doyle L, Chen W, Boivin O, et al.
bioRxiv
. 2023 Oct;
PMID: 37790440
Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing...
9.
Yeh A, Norn C, Kipnis Y, Tischer D, Pellock S, Evans D, et al.
Nature
. 2023 Feb;
614(7949):774-780.
PMID: 36813896
De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds, but has been...
10.
Lee S, Kim S, Lee G, Kwon S, Woo H, Seok C, et al.
Comput Struct Biotechnol J
. 2022 Dec;
21:158-167.
PMID: 36544468
While deep learning (DL) has brought a revolution in the protein structure prediction field, still an important question remains how the revolution can be transferred to advances in structure-based drug...