Protein-Ligand Binding Free-Energy Calculations with ARROW─A Purely First-Principles Parameterized Polarizable Force Field.

Autor: Nawrocki G; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Leontyev I; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Sakipov S; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Darkhovskiy M; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Kurnikov I; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Pereyaslavets L; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Kamath G; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Voronina E; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States.; Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia., Butin O; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Illarionov A; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Olevanov M; Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia., Kostikov A; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Ivahnenko I; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Patel DS; Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States., Sankaranarayanan SKRS; Center for Nanoscale Materials, Argonne National Lab, Lemont, Illinois 60439, United States.; Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, Illinois 60607, United States., Kurnikova MG; Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States., Lock C; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States.; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States., Crooks GE; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States., Levitt M; Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States., Kornberg RD; Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States., Fain B; InterX Inc., 805 Allston Way, Berkeley California, 94710, United States.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2022 Dec 13; Vol. 18 (12), pp. 7751-7763. Date of Electronic Publication: 2022 Dec 02.

Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote.

Autor: Kostygov, Alexei Yu.^1,2 (AUTHOR), Skýpalová, Karolína¹ (AUTHOR), Kraeva, Natalia¹ (AUTHOR), Kalita, Elora¹ (AUTHOR), McLeod, Cameron³ (AUTHOR), Yurchenko, Vyacheslav¹ (AUTHOR), Field, Mark C.^3,4 (AUTHOR), Lukeš, Julius^4,5 (AUTHOR), Butenko, Anzhelika^1,4,5 (AUTHOR) anzhelika.butenko@paru.cas.cz

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Performance limits of information engines.

Autor: du Buisson, Johan¹ (AUTHOR) johannes_du_buisson@sfu.ca, Sivak, David A.¹ (AUTHOR), Bechhoefer, John¹ (AUTHOR)

Publikováno v: Advances in Physics: X. Dec2024, Vol. 9 Issue 1, p1-31. 31p.

A novel in-silico model explores LanM homologs among Hyphomicrobium spp.

Autor: Valdés, James J.^1,2 (AUTHOR) valdes@paru.cas.cz, Petrash, Daniel A.^3,4 (AUTHOR) daniel.petras@geology.cz, Konhauser, Kurt O.⁵ (AUTHOR)

Publikováno v: Communications Biology. 11/20/2024, p1-11. 11p.

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Autor: Farias, André Borges^1,2 (AUTHOR) ernesto.perez@iimas.unam.mx, Martinez, Gustavo Sganzerla³ (AUTHOR), Galán-Vásquez, Edgardo⁴ (AUTHOR), Nicolás, Marisa Fabiana¹ (AUTHOR), Pérez-Rueda, Ernesto² (AUTHOR) ernesto.perez@iimas.unam.mx

Publikováno v: Briefings in Bioinformatics. Nov2024, Vol. 25 Issue 6, p1-12. 12p.