Zobrazeno 1 - 10
of 223
pro vyhledávání: '"Frank DiMaio"'
Autor:
Guangfeng Zhou, Domnita-Valeria Rusnac, Hahnbeom Park, Daniele Canzani, Hai Minh Nguyen, Lance Stewart, Matthew F. Bush, Phuong Tran Nguyen, Heike Wulff, Vladimir Yarov-Yarovoy, Ning Zheng, Frank DiMaio
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-14 (2024)
Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the
Externí odkaz:
https://doaj.org/article/29a1302972a44e30ab683de7520641e9
Autor:
Jared Adolf-Bryfogle, Jason W Labonte, John C Kraft, Maxim Shapovalov, Sebastian Raemisch, Thomas Lütteke, Frank DiMaio, Christopher D Bahl, Jesper Pallesen, Neil P King, Jeffrey J Gray, Daniel W Kulp, William R Schief
Publikováno v:
PLoS Computational Biology, Vol 20, Iss 6, p e1011895 (2024)
Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult. Computational approaches can aid in carbohydrate structure prediction, structure determinatio
Externí odkaz:
https://doaj.org/article/5de12898393041bbb087434f918ee19f
Autor:
Brandon J. Harris, Phuong T. Nguyen, Guangfeng Zhou, Heike Wulff, Frank DiMaio, Vladimir Yarov-Yarovoy
Publikováno v:
Frontiers in Pharmacology, Vol 15 (2024)
Ion channels are critical drug targets for a range of pathologies, such as epilepsy, pain, itch, autoimmunity, and cardiac arrhythmias. To develop effective and safe therapeutics, it is necessary to design small molecules with high potency and select
Externí odkaz:
https://doaj.org/article/90d203d05e0b492cb3d86bb0cfe56f93
Autor:
Anindya Roy, Lei Shi, Ashley Chang, Xianchi Dong, Andres Fernandez, John C. Kraft, Jing Li, Viet Q. Le, Rebecca Viazzo Winegar, Gerald Maxwell Cherf, Dean Slocum, P. Daniel Poulson, Garrett E. Casper, Mary L. Vallecillo-Zúniga, Jonard Corpuz Valdoz, Marcos C. Miranda, Hua Bai, Yakov Kipnis, Audrey Olshefsky, Tanu Priya, Lauren Carter, Rashmi Ravichandran, Cameron M. Chow, Max R. Johnson, Suna Cheng, McKaela Smith, Catherine Overed-Sayer, Donna K. Finch, David Lowe, Asim K. Bera, Gustavo Matute-Bello, Timothy P. Birkland, Frank DiMaio, Ganesh Raghu, Jennifer R. Cochran, Lance J. Stewart, Melody G. Campbell, Pam M. Van Ry, Timothy Springer, David Baker
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-18 (2023)
Abstract The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integri
Externí odkaz:
https://doaj.org/article/e3c311aafe5446188603fdc35eee2511
Autor:
Nathaniel R. Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne Vafeados, Ying Po Peng, Justas Dauparas, Minkyung Baek, Lance Stewart, Frank DiMaio, Steven De Munck, Savvas N. Savvides, David Baker
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-9 (2023)
Abstract 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 explo
Externí odkaz:
https://doaj.org/article/279adbbdbddf4e41bbd9f4a899f986cf
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-10 (2023)
As cryo-EM becomes commonplace in drug discovery, tools for automating small molecule structure determination are needed. Here, authors show a map-guided ligand modeling approach to building ligand structures at resolutions common in cryo-EM.
Externí odkaz:
https://doaj.org/article/53c8c4649db54047a2d734bb65fca8ed
Autor:
Julia Koehler Leman, Sergey Lyskov, Steven M. Lewis, Jared Adolf-Bryfogle, Rebecca F. Alford, Kyle Barlow, Ziv Ben-Aharon, Daniel Farrell, Jason Fell, William A. Hansen, Ameya Harmalkar, Jeliazko Jeliazkov, Georg Kuenze, Justyna D. Krys, Ajasja Ljubetič, Amanda L. Loshbaugh, Jack Maguire, Rocco Moretti, Vikram Khipple Mulligan, Morgan L. Nance, Phuong T. Nguyen, Shane Ó Conchúir, Shourya S. Roy Burman, Rituparna Samanta, Shannon T. Smith, Frank Teets, Johanna K. S. Tiemann, Andrew Watkins, Hope Woods, Brahm J. Yachnin, Christopher D. Bahl, Chris Bailey-Kellogg, David Baker, Rhiju Das, Frank DiMaio, Sagar D. Khare, Tanja Kortemme, Jason W. Labonte, Kresten Lindorff-Larsen, Jens Meiler, William Schief, Ora Schueler-Furman, Justin B. Siegel, Amelie Stein, Vladimir Yarov-Yarovoy, Brian Kuhlman, Andrew Leaver-Fay, Dominik Gront, Jeffrey J. Gray, Richard Bonneau
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-15 (2021)
Computational methods are becoming an increasingly important part of biological research. Using the Rosetta framework as an example, the authors demonstrate how community-driven development of computational methods can be done in a reproducible and r
Externí odkaz:
https://doaj.org/article/7ccba8c202cd473d906c246ef7b2eb77
Autor:
Daniel Mann, Junping Fan, Kamolrat Somboon, Daniel P. Farrell, Andrew Muenks, Svetomir B. Tzokov, Frank DiMaio, Syma Khalid, Samuel I. Miller, Julien R. C. Bergeron
Publikováno v:
Communications Biology, Vol 4, Iss 1, Pp 1-9 (2021)
Daniel Mann et al. describe a higher-resolution structure of the maintenance of lipid asymmetry inner membrane complex (MlaBDEF) in the Gram-negative pathogen, Acinetobacter baumannii. With this improved structural map, the authors clarify the second
Externí odkaz:
https://doaj.org/article/85d066ee80af486582adf7e304e0d791
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-13 (2021)
Sea urchin hyperpolarization-activated cyclic nucleotide-gated (spHCN) ion channels channels are activated by membrane hyperpolarization instead of depolarization and undergo inactivation with hyperpolarization. Here authors apply transition metal io
Externí odkaz:
https://doaj.org/article/87335df92b7c4bdb83eb77f703536c2b
Autor:
Daniel P. Farrell, Ivan Anishchenko, Shabih Shakeel, Anna Lauko, Lori A. Passmore, David Baker, Frank DiMaio
Publikováno v:
IUCrJ, Vol 7, Iss 5, Pp 881-892 (2020)
Cryo-electron microscopy of protein complexes often leads to moderate resolution maps (4–8 Å), with visible secondary-structure elements but poorly resolved loops, making model building challenging. In the absence of high-resolution structures of
Externí odkaz:
https://doaj.org/article/1da6a191c75943b3abff254cb90cbef5