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Article: De novo

Wallace, Hailey M / Yang, Hyunjun / Tan, Sophia / Pan, Henry S / Yang, Rose / Xu, Junyi / Jo, Hyunil / Condello, Carlo / Polizzi, Nicholas F / DeGrado, William F

bioRxiv : the preprint server for biology

2023

Abstract: Insoluble amyloids rich in cross-β fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to ... ...

Abstract	Insoluble amyloids rich in cross-β fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloid in a conformationally specific manner are lacking. We introduce a novel computational method for
Language	English
Publishing date	2023-11-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.14.567090
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: De novo

Lu, Lei / Gou, Xuxu / Tan, Sophia K / Mann, Samuel I / Yang, Hyunjun / Zhong, Xiaofang / Gazgalis, Dimitrios / Valdiviezo, Jesús / Jo, Hyunil / Wu, Yibing / Diolaiti, Morgan E / Ashworth, Alan / Polizzi, Nicholas F / DeGrado, William F

bioRxiv : the preprint server for biology

2023

Abstract: The de novo design of small-molecule-binding proteins has seen exciting recent progress ... suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now ...

Abstract	The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low μM, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles.
Language	English
Publishing date	2023-12-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.23.573178
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: De novo

Chen, Yuyang / Dawes, Ruebena / Kim, Hyung Chul / Stenton, Sarah L / Walker, Susan / Ljungdahl, Alicia / Lord, Jenny / Ganesh, Vijay S / Ma, Jialan / Martin-Geary, Alexandra C / Lemire, Gabrielle / D'Souza, Elston N / Dong, Shan / Ellingford, Jamie M / Adams, David R / Allan, Kirsten / Bakshi, Madhura / Baldwin, Erin E / Berger, Seth I /

Bernstein, Jonathan A / Brown, Natasha J / Burrage, Lindsay C / Chapman, Kimberly / Compton, Alison G / Cunningham, Chloe A / D'Souza, Precilla / Délot, Emmanuèle C / Dias, Kerith-Rae / Elias, Ellen R / Evans, Carey-Anne / Ewans, Lisa / Ezell, Kimberly / Fraser, Jamie L / Gallacher, Lyndon / Genetti, Casie A / Grant, Christina L / Haack, Tobias / Kuechler, Alma / Lalani, Seema R / Leitão, Elsa / Fevre, Anna Le / Leventer, Richard J / Liebelt, Jan E / Lockhart, Paul J / Ma, Alan S / Macnamara, Ellen F / Maurer, Taylor M / Mendez, Hector R / Montgomery, Stephen B / Nassogne, Marie-Cécile / Neumann, Serena / O'Leary, Melanie / Palmer, Elizabeth E / Phillips, John / Pitsava, Georgia / Pysar, Ryan / Rehm, Heidi L / Reuter, Chloe M / Revencu, Nicole / Riess, Angelika / Rius, Rocio / Rodan, Lance / Roscioli, Tony / Rosenfeld, Jill A / Sachdev, Rani / Simons, Cas / Sisodiya, Sanjay M / Snell, Penny / Clair, Laura / Stark, Zornitza / Tan, Tiong Yang / Tan, Natalie B / Temple, Suzanna El / Thorburn, David R / Tifft, Cynthia J / Uebergang, Eloise / VanNoy, Grace E / Vilain, Eric / Viskochil, David H / Wedd, Laura / Wheeler, Matthew T / White, Susan M / Wojcik, Monica / Wolfe, Lynne A / Wolfenson, Zoe / Xiao, Changrui / Zocche, David / Rubenstein, John L / Markenscoff-Papadimitriou, Eirene / Fica, Sebastian M / Baralle, Diana / Depienne, Christel / MacArthur, Daniel G / Howson, Joanna Mm / Sanders, Stephan J / O'Donnell-Luria, Anne / Whiffin, Nicola

medRxiv : the preprint server for health sciences

2024

Abstract: Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding ... ...

Abstract	Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.07.24305438
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Article ; Online: De Novo

Lin, Zedong / Yang, Zhenhai / Wang, Jian / Yang, Shihe

ACS applied materials & interfaces

2023

Abstract: Self-driven narrowband perovskite photodetectors have recently attracted significant attention due to their simple preparation, high performance, and amenability for system integration. However, the origin of narrowband photoresponse and the related ... ...

Abstract	Self-driven narrowband perovskite photodetectors have recently attracted significant attention due to their simple preparation, high performance, and amenability for system integration. However, the origin of narrowband photoresponse and the related regulation mechanisms still remains elusive. To address these issues, we herein perform a systematic investigation by formulating an analytic model in conjunction with finite element simulation. The optical and electrical simulations have resulted in design principles for perovskite narrowband photodetectors in terms of the dependence of external quantum efficiency (EQE) on perovskite layer thickness, doping concentration, and band gap as well as trap state concentration. Careful investigations on the profiles of electric field, current, and optical absorption reveal the dependence of narrowband EQE on the direction of incident light and perovskite doping types: only p-type perovskite can yield the narrowband photoresponse for illumination from the hole transport layer (HTL) side. The simulation results demonstrated in this study shed new light on the mechanism of perovskite-based narrowband photodetectors and provide valuable guidance for their design.
Language	English
Publishing date	2023-03-09
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.2c22904
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: De novo

Li, Jingjing / Wang, Haiyan / Zhu, Jianqing / Yang, Qi / Luan, Yang / Shi, Leming / Molina-Mora, José Arturo / Zheng, Yuanting

Frontiers in genetics

2023 Volume 14, Page(s) 1107353

Abstract: Sericinus ... ...

Abstract	Sericinus montelus
Language	English
Publishing date	2023-03-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1107353
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Article ; Online: De novo

Tan, Zheng / Li, Yan / Wu, Xin / Zhang, Ziying / Shi, Weimei / Yang, Shiqing / Zhang, Wanli

RSC advances

2023 Volume 13, Issue 2, Page(s) 1031–1040

Abstract: The development of AI for fluorescent materials design is technologically demanding due to the issue of accurately forecasting fluorescent properties. Besides the huge efforts made in predicting the photoluminescent properties of organic dyes in terms of ...

Abstract	The development of AI for fluorescent materials design is technologically demanding due to the issue of accurately forecasting fluorescent properties. Besides the huge efforts made in predicting the photoluminescent properties of organic dyes in terms of machine learning techniques, this article aims to introduce an adversarial generation paradigm for the rational design of fluorescent molecules. Molecular SMILES is employed as the input of a GRU based autoencoder, where the encoding and decoding of the string information are processed. A generative adversarial network is applied on the latent space with a generator to generate samples to mimic the latent space, and a discriminator to distinguish samples from the latent space. It is found that the excited state property distributions of generated molecules fully match those of the original samples, with the molecular synthesizability being accessible as well. Further screening of the generated samples delivers a remarkable luminescence efficiency of molecules epitomized by the significant oscillator strength and charge transfer characteristics, demonstrating the great potential of the adversarial model in enriching the fluorescent library.
Language	English
Publishing date	2023-01-04
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d2ra07008a
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Article ; Online: De novo

Gao, Hongyang / Zhang, Huiju / Hu, Yuqing / Xu, Danyun / Zheng, Sikai / Su, Shuting / Yang, Quan

Chinese herbal medicines

2023 Volume 15, Issue 2, Page(s) 310–316

Abstract: Objective: The barks, leaves, and branches of : Methods: Chemical analysis, metabolome sequencing, and transcriptome sequencing were performed to investigate the molecular mechanisms underlying the difference of active components content in the barks, ...

Abstract	Objective: The barks, leaves, and branches of Methods: Chemical analysis, metabolome sequencing, and transcriptome sequencing were performed to investigate the molecular mechanisms underlying the difference of active components content in the barks, branches and leaves of Results: Metabolomic analysis revealed that small amounts of flavonoids, coumarine, and cinnamaldehyde accumulated in both leaves and branches. Transcriptome analysis showed that genes associated with phenylpropanoid and flavonoid biosynthesis were downregulated in the leaves and branches relative to the barks. The observed differences in essential oil content among the three tissues may be attributable to the differential expression of genes involved in the phenylpropanoid and flavonoid metabolic pathways. Conclusion: This study identified the key genes in the phenylpropanoid pathway controling the flavonoid, coumarine, and cinnamaldehyde contents in the barks, branches and leaves by comparing the transcriptome and metabolome
Language	English
Publishing date	2023-02-16
Publishing country	Singapore
Document type	Journal Article
ISSN	2589-3610
ISSN (online)	2589-3610
DOI	10.1016/j.chmed.2022.06.013
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Article: De novo

Wei, Juan / Papanastasiou, Dimitris / Kosmopoulou, Mariangela / Smyrnakis, Athanasios / Hong, Pengyu / Tursumamat, Nafisa / Klein, Joshua A / Xia, Chaoshuang / Tang, Yang / Zaia, Joseph / Costello, Catherine E / Lin, Cheng

Chemical science

2023 Volume 14, Issue 24, Page(s) 6695–6704

Abstract: ... ...

Abstract	Comprehensive
Language	English
Publishing date	2023-06-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d3sc00870c
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Article ; Online: De novo

Yang, Jinyue / Zhang, Xueting / Dong, Junhua / Zhang, Qian / Sun, Erchao / Chen, Cen / Miao, Zhuangxia / Zheng, Yifei / Zhang, Nan / Tao, Pan

Frontiers in immunology

2023 Volume 14, Page(s) 1274027

Abstract: Background: Emerging infectious diseases pose a significant threat to both human and animal populations. Rapid : Methods: Here, we focused on : Results: As a proof of concept, we identified 3 novel protective proteins of : Discussion: We ... ...

Abstract	Background: Emerging infectious diseases pose a significant threat to both human and animal populations. Rapid Methods: Here, we focused on Results: As a proof of concept, we identified 3 novel protective proteins of Discussion: We believe that our strategy can be applied to any bacterial pathogen and has the potential to significantly accelerate the development of antigen-matched vaccines to prevent the spread of an emerging novel bacterial pathogen.
MeSH term(s)	Animals ; Humans ; Swine ; Antigens, Bacterial ; Bacterial Vaccines ; Bacterial Proteins ; Pleuropneumonia/microbiology ; Pleuropneumonia/prevention & control ; Actinobacillus pleuropneumoniae
Chemical Substances	Antigens, Bacterial ; Bacterial Vaccines ; Bacterial Proteins
Language	English
Publishing date	2023-11-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1274027
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Article: De novo

Jiang, Hanlun / Jude, Kevin M / Wu, Kejia / Fallas, Jorge / Ueda, George / Brunette, T J / Hicks, Derrick / Pyles, Harley / Yang, Aerin / Carter, Lauren / Lamb, Mila / Li, Xinting / Levine, Paul M / Stewart, Lance / Garcia, K Christopher / Baker, David

bioRxiv : the preprint server for biology

2023

Abstract: In natural proteins, structured loops play central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein ... ...

Abstract	In natural proteins, structured loops play central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by
Language	English
Publishing date	2023-08-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.22.554384
Database	MEDical Literature Analysis and Retrieval System OnLINE

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