Recent Advances in Simulation Software and Force Fields: Their Importance in Theoretical and Computational Chemistry and Biophysics.

Autor: Chipot C; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, UMR n°7019, Université de Lorraine, 54506 Vandoeuvre-lès-Nancy cedex, France.; Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2024 Dec 12; Vol. 128 (49), pp. 12023-12026.

Expanded Functionality and Portability for the Colvars Library.

Autor: Fiorin G; National Institute of Neurological Disorders and Stroke, Bethesda, Maryland 20814, United States.; National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States., Marinelli F; National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States.; Department of Biophysics and Data Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, United States., Forrest LR; National Institute of Neurological Disorders and Stroke, Bethesda, Maryland 20814, United States., Chen H; Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States., Chipot C; Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States.; Laboratoire International Associé CNRS et University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy, France.; Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States.; Department of Chemistry, The University of Hawai'i at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States., Kohlmeyer A; Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States., Santuz H; Laboratoire de Biochimie Théorique UPR 9080, Université Paris Cité, CNRS, 75005 Paris, France., Hénin J; Laboratoire de Biochimie Théorique UPR 9080, Université Paris Cité, CNRS, 75005 Paris, France.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2024 Nov 14; Vol. 128 (45), pp. 11108-11123. Date of Electronic Publication: 2024 Nov 05.

Elucidation of the noncovalent interactions driving enzyme activity guides branching enzyme engineering for α-glucan modification.

Autor: Zong Z; National Engineering Research Center of Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. zongzhy@tib.cas.cn.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China. zongzhy@tib.cas.cn., Zhang X; National Engineering Research Center of Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China., Chen P; National Engineering Research Center of Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China., Fu Z; National Engineering Research Center of Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China., Zeng Y; National Engineering Research Center of Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China., Wang Q; National Engineering Research Center of Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China., Chipot C; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Université de Lorraine CNRS, Vandœuvre-lès-Nancy, France.; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA.; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, USA., Leggio LL; Department of Chemistry, University of Copenhagen, Copenhagen, Denmark., Sun Y; National Engineering Research Center of Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. sun_yx@tib.cas.cn.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China. sun_yx@tib.cas.cn.

Publikováno v: Nature communications [Nat Commun] 2024 Oct 09; Vol. 15 (1), pp. 8760. Date of Electronic Publication: 2024 Oct 09.

Statistical Mechanical Theories of Membrane Permeability.

Autor: Harris J; Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States., Chipot C; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Université de Lorraine, Unité Mixte de Recherche n7019, B.P. 70239, 54506 cedex Vandœuvre-lès-Nancy, France.; Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.; Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States., Roux B; Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2024 Sep 26; Vol. 128 (38), pp. 9183-9196. Date of Electronic Publication: 2024 Sep 16.

Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT 3 receptors.

Autor: López-Sánchez U; University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.; Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA., Munro LJ; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark., Ladefoged LK; Department of Chemistry, Aarhus University, Aarhus, Denmark., Pedersen AJ; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark., Brun CC; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark., Lyngby SM; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark., Baud D; University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France., Juillan-Binard C; University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France., Pedersen MG; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark., Lummis SCR; Department of Biochemistry, University of Cambridge, Cambridge, UK., Bang-Andersen B; Lundbeck Research, H. Lundbeck A/S, Valby, Denmark., Schiøtt B; Department of Chemistry, Aarhus University, Aarhus, Denmark., Chipot C; Université de Lorraine, CNRS, LPCT, Nancy, France.; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France.; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Schoehn G; University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France., Neyton J; University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France., Dehez F; Université de Lorraine, CNRS, LPCT, Nancy, France.; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France., Nury H; University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France. hugues.nury@ibs.fr., Kristensen AS; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark. ask@sund.ku.dk.

Publikováno v: Nature structural & molecular biology [Nat Struct Mol Biol] 2024 Aug; Vol. 31 (8), pp. 1232-1242. Date of Electronic Publication: 2024 May 02.