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Distance-based Protein Folding Powered by Deep Learning [PDF]

Proceedings of the National Academy of Sciences of the United States of America, 2018
Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed to predict ...
Xu, Jinbo
core   +2 more sources

ColabFold: making protein folding accessible to all

Nature Methods, 2022
ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold.
M. Mirdita, S. Ovchinnikov, Martin Steinegger   +2 more
semanticscholar   +1 more source

Protein structure generation via folding diffusion [PDF]

Nature Communications, 2022
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases.
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, James Zou, Alex X. Lu, Ava P. Amini   +5 more
semanticscholar   +1 more source

Harnessing protein folding neural networks for peptide–protein docking

Nature Communications, 2021
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have tremendous impact on structural biology and beyond.
Tomer Tsaban, Julia K. Varga, O. Avraham, Ziv Ben-Aharon, A. Khramushin, Ora Schueler‐Furman   +5 more
semanticscholar   +1 more source

Pathologic tau conformer ensembles induce dynamic, liquid-liquid phase separation events at the nuclear envelope

BMC Biology, 2021
Background The microtubule-associated protein tau forms aggregates in different neurodegenerative diseases called tauopathies. Prior work has shown that a single P301L mutation in tau gene, MAPT, can promote alternative tau folding pathways that ...
Sang-Gyun Kang, Zhuang Zhuang Han, Nathalie Daude, Emily McNamara, Serene Wohlgemuth, Laura Molina-Porcel, Jiri G. Safar, Sue-Ann Mok, David Westaway   +8 more
doaj   +1 more source

Innate Immune Status of Glia Modulates Prion Propagation in Early Stage of Infection

Cells, 2023
Prion diseases are progressive neurodegenerative disorders affecting humans and various mammals. The prominent neuropathological change in prion-affected brains is neuroinflammation, histopathologically characterized by reactive gliosis surrounding prion
Sang-Gyun Kang, Chiye Kim, Judd Aiken, Debbie McKenzie   +3 more
doaj   +1 more source

The measurement of true initial rates is not always absolutely necessary to estimate enzyme kinetic parameters

Scientific Reports, 2023
In the chapters dealing with enzyme reactions, the authors of all Biochemistry textbooks and of even more specialized texts consider that the characteristic parameters (k cat and K m ) must be determined under initial or steady-state rate conditions ...
Jean-Marie Frère, Olivier Verlaine, André Matagne   +2 more
doaj   +1 more source

Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway [PDF]

, 2014
In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding).
A Jansens, A Land, A Pirneskoski, A. Katrine Wallis, Alistair G. Irvine, AR Karala, AR Karala, AY Denisov, B van den Berg, B van den Berg, B van den Berg, CB Anfinsen, Claudia A. Blindauer, CPM van Mierlo, CPM van Mierlo, CW Gruber, DP Goldenberg, E van Anken, F Hatahet, G Kozlov, G Wagner, HC Shin, HC Shin, J Riemer, JH Laity, JL Arolas, JS Weissman, JS Weissman, L Wang, LJ Byrne, Lloyd W. Ruddock, M Narayan, Mark J. Howard, Michelle L. Rowe, Narinder Sanghera, NJ Bulleid, NJ Darby, P Klappa, P Venetianer, RA Williamson, RB Freedman, RF Goldberger, Richard A. Williamson, RJ Ellis, Robert B. Freedman, S Masui, S Talluri, Salvador Ventura, TE Creighton, TE Creighton, TE Creighton, TE Creighton, VD Nguyen, VD Nguyen, WF Vranken   +54 more
core   +7 more sources

Susceptibility of Beavers to Chronic Wasting Disease

Biology, 2022
Chronic wasting disease (CWD) is a contagious, fatal, neurodegenerative prion disease of cervids. The expanding geographical range and rising prevalence of CWD are increasing the risk of pathogen transfer and spillover of CWD to non-cervid sympatric ...
Allen Herbst, Serene Wohlgemuth, Jing Yang, Andrew R. Castle, Diana Martinez Moreno, Alicia Otero, Judd M. Aiken, David Westaway, Debbie McKenzie   +8 more
doaj   +1 more source

Unconjugated PLGA nanoparticles attenuate temperature-dependent β-amyloid aggregation and protect neurons against toxicity: implications for Alzheimer’s disease pathology

Journal of Nanobiotechnology, 2022
Conversion of β-amyloid (Aβ) peptides from soluble random-coil to aggregated protein enriched with β-sheet-rich intermediates has been suggested to play a role in the degeneration of neurons and development of Alzheimer’s disease (AD) pathology ...
Pallabi Sil Paul, Jae-Young Cho, Qi Wu, Govindarajan Karthivashan, Emily Grabovac, Holger Wille, Mariana Kulka, Satyabrata Kar   +7 more
doaj   +1 more source