BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery

Autor: John, Peter St., Lin, Dejun, Binder, Polina, Greaves, Malcolm, Shah, Vega, John, John St., Lange, Adrian, Hsu, Patrick, Illango, Rajesh, Ramanathan, Arvind, Anandkumar, Anima, Brookes, David H, Busia, Akosua, Mahajan, Abhishaike, Malina, Stephen, Prasad, Neha, Sinai, Sam, Edwards, Lindsay, Gaudelet, Thomas, Regep, Cristian, Steinegger, Martin, Rost, Burkhard, Brace, Alexander, Hippe, Kyle, Naef, Luca, Kamata, Keisuke, Armstrong, George, Boyd, Kevin, Cao, Zhonglin, Chou, Han-Yi, Chu, Simon, Costa, Allan dos Santos, Darabi, Sajad, Dawson, Eric, Didi, Kieran, Fu, Cong, Geiger, Mario, Gill, Michelle, Hsu, Darren, Kaushik, Gagan, Korshunova, Maria, Kothen-Hill, Steven, Lee, Youhan, Liu, Meng, Livne, Micha, McClure, Zachary, Mitchell, Jonathan, Moradzadeh, Alireza, Mosafi, Ohad, Nashed, Youssef, Paliwal, Saee, Peng, Yuxing, Rabhi, Sara, Ramezanghorbani, Farhad, Reidenbach, Danny, Ricketts, Camir, Roland, Brian, Shah, Kushal, Shimko, Tyler, Sirelkhatim, Hassan, Srinivasan, Savitha, Stern, Abraham C, Toczydlowska, Dorota, Veccham, Srimukh Prasad, Venanzi, Niccolò Alberto Elia, Vorontsov, Anton, Wilber, Jared, Wilkinson, Isabel, Wong, Wei Jing, Xue, Eva, Ye, Cory, Yu, Xin, Zhang, Yang, Zhou, Guoqing, Zandstein, Becca, Dallago, Christian, Trentini, Bruno, Kucukbenli, Emine, Rvachov, Timur, Calleja, Eddie, Israeli, Johnny, Clifford, Harry, Haukioja, Risto, Haemel, Nicholas, Tretina, Kyle, Tadimeti, Neha, Costa, Anthony B

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language mode

Externí odkaz: http://arxiv.org/abs/2411.10548

Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis

Autor: Eric P. Knoshaug, Peipei Sun, Ambarish Nag, Huong Nguyen, Erin M. Mattoon, Ningning Zhang, Jian Liu, Chen Chen, Jianlin Cheng, Ru Zhang, Peter St. John, James Umen

Publikováno v: Plant Direct, Vol 7, Iss 12, Pp n/a-n/a (2023)

Abstract The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome‐wide protein‐coding gene annotation. A substantial fraction of protein‐coding genes in all plant genomes are poorly

Externí odkaz: https://doaj.org/article/d9b248442fe74e0880ef74960f273da3

Biomolecular condensate phase diagrams with a combinatorial microdroplet platform

Autor: William E. Arter, Runzhang Qi, Nadia A. Erkamp, Georg Krainer, Kieran Didi, Timothy J. Welsh, Julia Acker, Jonathan Nixon-Abell, Seema Qamar, Jordina Guillén-Boixet, Titus M. Franzmann, David Kuster, Anthony A. Hyman, Alexander Borodavka, Peter St George-Hyslop, Simon Alberti, Tuomas P. J. Knowles

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-10 (2022)

A central concept for characterising phase-separating systems is the phase diagram but generation of such diagrams for biomolecular systems is typically slow and low-throughput. Here the authors describe PhaseScan, a combinatorial droplet microfluidi

Externí odkaz: https://doaj.org/article/21a365c2a2af4ba08de716204af10bed

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Autor: Georg Krainer, Timothy J. Welsh, Jerelle A. Joseph, Jorge R. Espinosa, Sina Wittmann, Ella de Csilléry, Akshay Sridhar, Zenon Toprakcioglu, Giedre Gudiškytė, Magdalena A. Czekalska, William E. Arter, Jordina Guillén-Boixet, Titus M. Franzmann, Seema Qamar, Peter St George-Hyslop, Anthony A. Hyman, Rosana Collepardo-Guevara, Simon Alberti, Tuomas P. J. Knowles

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

Elucidating the molecular driving forces underlying liquid–liquid phase separation is a key objective for understanding biological function and malfunction. Here the authors show that a wide range of cellular proteins, including FUS, TDP-43, Brd4,

Externí odkaz: https://doaj.org/article/f1a7c13511ed46d3b7d48b9f4017a81c

Does Soluble TREM2 Protect Against Alzheimer's Disease?

Autor: Guy C. Brown, Peter St George-Hyslop

Publikováno v: Frontiers in Aging Neuroscience, Vol 13 (2022)

Triggering Receptor Expressed in Myeloid Cells 2 (TREM2) is a pattern recognition receptor on myeloid cells, and is upregulated on microglia surrounding amyloid plaques in Alzheimer's disease (AD). Rare, heterozygous mutations in TREM2 (e.g., R47H) i

Externí odkaz: https://doaj.org/article/7cc45101dffe4ce69d803f10df62d3fc