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Mar 20, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
S. Wang, S. Sun, Z. Li, R. Zhang, J. Xu, Accurate de novo prediction of protein contact map by ultra-deep learning model. PLOS Comput. Biol. 13, e1005324 (2017). J. Xu, Distance-based protein folding powered by deep learning. Proc. Natl. Acad. Sci. U.S.A. 116, 16856–16865 (2019). M. Akdel et al., A structural biology community assessment of AlphaFold2 applications. Nat. Struct. Mol. Biol. 29, 1056–1067 (2022). G. R. Buel, K. J. Walters, Can AlphaFold2 predict the impact of missense mutations on structure? Nat. Struct. Mol.
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Mar 20, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
Myosin-5 varies its step length to carry cargo straight along the irregular F-actin trackAdam Fineberg https://orcid.org/0000-0002-6808-1818, Yasuharu Takagi [email protected], Kavitha Thirumurugan https://orcid.org/0000-0002-4673-4099, +9 , Joanna Andrecka, Neil Billington, Gavin Young, Daniel Cole, Stan A. Burgess, Alistair P. Curd https://orcid.org/0000-0002-3949-7523, John A. Hammer, James R. Sellers https://orcid.org/0000-0001-6296-564X, Philipp Kukura [email protected], and Peter J.
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Mar 20, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
SignificanceComputational protein structure prediction has been significantly improved by the application of coevolution information derived from multiple sequence alignment (MSA) and deep learning. Although very powerful, these methods do not perform well on small-sized protein families, flexible regions such as highly variable antibody Complementarity-determining region (CDR) regions, and single mutation effects.
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Mar 20, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transportDanila Boytsov https://orcid.org/0000-0002-6200-7158, Gregor M. Madej https://orcid.org/0000-0001-9181-6387, Georg Horn, +6 , Nadine Blaha, Thomas Köcher, Harald H.
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Mar 19, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
Isotype switching in human memory B cells sets intrinsic antigen-affinity thresholds that dictate antigen-driven fatesEdited by Mark Davis, Stanford University School of Medicine, Palo Alto, CA; received August 14, 2023; accepted January 30, 2024SignificanceIn an era of predicted recurring pandemics, the ability to produce highly effective vaccines that provide long-lived protection from pathogens and their mutant variants will be critical.
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Mar 19, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
D. Braess, Über ein paradoxon aus der verkehrsplanung. Unternehmensforschung 12, 258–268 (1968). T. Roughgarden, Selfish Routing and the Price of Anarchy (MIT Press, 2005). O. Kim, M. Walker, The free rider problem: Experimental evidence. Public Choice 43, 3–24 (1984). R. Albanese, D. D. Van Fleet, Rational behavior in groups: The free-riding tendency. Acad. Manage. Rev. 10, 244–255 (1985). L. A. Giraldeau, F. Dubois, Social foraging and the study of exploitative behavior. Adv. Study Behav. 38, 59–104 (2008). K.
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Mar 19, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
Steering lithium and potassium storage mechanism in covalent organic frameworks by incorporating transition metal single atoms Yingnan Cao https://orcid.org/0009-0005-2659-6281, Qing Xu https://orcid.org/0000-0002-9066-9837, Yi Sun https://orcid.org/0000-0001-6175-9350, +8 , Jixin Shi https://orcid.org/0009-0004-5608-4239, Yi Xu, Yongfu Tang, Xiudong Chen, Shuai Yang, Zheng Jiang, Han-Don Um, Xiaopeng Li [email protected], and Yong Wang [email protected] -8Authors Info & Affiliations...
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Mar 19, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
Vulnerability to APOBEC3G linked to the pathogenicity of deltaretroviruses Takafumi Shichijo https://orcid.org/0000-0002-1272-3738, Jun-ichirou Yasunaga https://orcid.org/0000-0002-7939-2080 [email protected], Kei Sato https://orcid.org/0000-0003-4431-1380, +12 , Kisato Nosaka https://orcid.org/0000-0001-6682-2451, Kosuke Toyoda https://orcid.org/0000-0001-8125-4528, Miho Watanabe https://orcid.org/0009-0002-0764-2287, Wenyi Zhang https://orcid.org/0009-0006-9885-411X, Yoshio...
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Mar 19, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
Dual topologies of myotomal collagen XV and Tenascin C act in concert to guide and shape developing motor axons Laurie Nemoz-Billet, Martial Balland, Laurent Gilquin, +12 , Benjamin Gillet https://orcid.org/0000-0002-6610-4537, Isabelle Stévant, Emilie Guillon, Sandrine Hughes https://orcid.org/0000-0003-3932-9180, Gilles Carpentier https://orcid.org/0000-0002-3730-7263, Elisabeth Vaganay, Frédéric Sohm https://orcid.org/0000-0002-6227-9436, Vladimir Misiak...
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Mar 18, 2024 | 
pnas.org | Amanda Giang |Morgan Edwards |Sarah Fletcher |Rivkah Gardner-Frolick
G. Nicolis, C. Nicolis, Foundations of Complex Systems: Emergence, Information and Prediction (World Scientific, 2012). J. Kwapień, S. Drożdż, Physical approach to complex systems. Phys. Rep. 515, 115–226 (2012). H. Matsuda, Physical nature of higher-order mutual information: Intrinsic correlations and frustration. Phys. Rev. E 62, 3096 (2000). M. Koch-Janusz, Z. Ringel, Mutual information, neural networks and the renormalization group. Nat. Phys. 14, 578–582 (2018). P.
