Cargando…

Improving de novo protein binder design with deep learning

Recently it has become possible to de novo design high affinity protein binding proteins from target structural information alone. There is, however, considerable room for improvement as the overall design success rate is low. Here, we explore the augmentation of energy-based protein binder design u...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bennett, Nathaniel R., Coventry, Brian, Goreshnik, Inna, Huang, Buwei, Allen, Aza, Vafeados, Dionne, Peng, Ying Po, Dauparas, Justas, Baek, Minkyung, Stewart, Lance, DiMaio, Frank, De Munck, Steven, Savvides, Savvas N., Baker, David
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2023
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10163288/ https://www.ncbi.nlm.nih.gov/pubmed/37149653 http://dx.doi.org/10.1038/s41467-023-38328-5

Ejemplares similares

Improved protein structure refinement guided by deep learning based accuracy estimation
por: Hiranuma, Naozumi, et al.
Publicado: (2021)

Peptide-binding specificity prediction using fine-tuned protein structure prediction networks
por: Motmaen, Amir, et al.
Publicado: (2023)

Computational design of sequence-specific DNA-binding proteins
por: Glasscock, Cameron J., et al.
Publicado: (2023)

An enumerative algorithm for de novo design of proteins with diverse pocket structures
por: Basanta, Benjamin, et al.
Publicado: (2020)

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
por: Cao, Longxing, et al.
Publicado: (2020)

Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14
por: Anishchenko, Ivan, et al.
Publicado: (2021)

De novo design of luciferases using deep learning
por: Yeh, Andy Hsien-Wei, et al.
Publicado: (2023)

Scaffolding protein functional sites using deep learning
por: Wang, Jue, et al.
Publicado: (2022)

Transferrin receptor targeting by de novo sheet extension
por: Sahtoe, Danny D., et al.
Publicado: (2021)

Design of protein-binding proteins from the target structure alone
por: Cao, Longxing, et al.
Publicado: (2022)

De novo design of protein structure and function with RFdiffusion
por: Watson, Joseph L., et al.
Publicado: (2023)

Designed Endocytosis-Triggering Proteins mediate Targeted Degradation
por: Huang, Buwei, et al.
Publicado: (2023)

Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis
por: Kozak, Sandra, et al.
Publicado: (2020)

De novo protein structure determination from near-atomic resolution cryo-EM maps
por: Wang, Ray Yu-Ruei, et al.
Publicado: (2015)

Self-organization of swimmers drives long-range fluid transport in bacterial colonies
por: Xu, Haoran, et al.
Publicado: (2019)

Computational design of a synthetic PD-1 agonist
por: Bryan, Cassie M., et al.
Publicado: (2021)

Synthesis and characterization of carboxylated PBAMO copolymers as promising prepolymers for energetic binders
por: Lim, Minkyung, et al.
Publicado: (2020)

De novo design of modular peptide-binding proteins by superhelical matching
por: Wu, Kejia, et al.
Publicado: (2023)

Precise assembly of complex beta sheet topologies from de novo designed building blocks
por: King, Indigo Chris, et al.
Publicado: (2015)

Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention
por: Bhattacharya, Nicholas, et al.
Publicado: (2022)

De novo designed Hsp70 activator dissolves intracellular condensates
por: Zhang, Jason Z, et al.
Publicado: (2023)

Modulation of Signaling Mediated by TSLP and IL-7 in Inflammation, Autoimmune Diseases, and Cancer
por: Marković, Iva, et al.
Publicado: (2020)

Hallucinating symmetric protein assemblies
por: Wicky, B. I. M., et al.
Publicado: (2022)

De Novo Discovery of High-Affinity Peptide Binders for the SARS-CoV-2 Spike Protein
por: Pomplun, Sebastian, et al.
Publicado: (2020)

De novo protein design by citizen scientists
por: Koepnick, Brian, et al.
Publicado: (2019)

Engineering and crystal structure of a monomeric FLT3 ligand variant
por: Pannecoucke, Erwin, et al.
Publicado: (2021)

Randomized gates eliminate bias in sort‐seq assays
por: Trippe, Brian L., et al.
Publicado: (2022)

Single-Chain Soluble Receptor Fusion Proteins as Versatile Cytokine Inhibitors
por: Holgado, Aurora, et al.
Publicado: (2020)

The War on Cancer: An Update from the New Haven Theater of Operations
por: DiMaio, Daniel
Publicado: (2007)

Is Virology Dead?
por: DiMaio, Daniel
Publicado: (2014)

Nuns, Warts, Viruses, and Cancer
por: DiMaio, Daniel
Publicado: (2015)

Thank You, Edward. Merci, Louis.
por: DiMaio, Daniel
Publicado: (2016)

Advances in Rosetta structure prediction for difficult molecular-replacement problems
por: DiMaio, Frank
Publicado: (2013)

Low Formaldehyde Binders for Mineral Wool Insulation: A Review
por: Bennett, Thomas M., et al.
Publicado: (2022)

Binders: In a nutshell
por: Bhattacharya, S., et al.
Publicado: (2012)

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins
por: Gerben, Stacey R, et al.
Publicado: (2023)

De novo design of protein homodimers containing tunable symmetric protein pockets
por: Hicks, Derrick R., et al.
Publicado: (2022)

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman
por: Petti, Samantha, et al.
Publicado: (2022)

Structures and disulfide cross‐linking of de novo designed therapeutic mini‐proteins
por: Silva, Daniel‐Adriano, et al.
Publicado: (2018)

Delineation of the Pasteurellaceae-specific GbpA-family of glutathione-binding proteins
por: Vergauwen, Bjorn, et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_i67v8o9e19s7153uqfimu2gnaa