Machine-learned molecular mechanics force fields from large-scale quantum chemical data.

Autor: Takaba K; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.; Pharmaceuticals Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation Shizuoka 410-2321 Japan takaba.kb@om.asahi-kasei.co.jp., Friedman AJ; Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA., Cavender CE; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA., Behara PK; Center for Neurotherapeutics, Department of Pathology and Laboratory Medicine, University of California Irvine CA 92697 USA., Pulido I; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., Henry MM; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., MacDermott-Opeskin H; Open Molecular Software Foundation Davis CA 95618 USA., Iacovella CR; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., Nagle AM; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.; Department of Bioengineering, University of California, Berkeley Berkeley CA 94720 USA., Payne AM; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.; Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center New York 10065 USA., Shirts MR; Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA., Mobley DL; Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., Wang Y; Simons Center for Computational Physical Chemistry and Center for Data Science, New York University New York NY 10004 USA.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.

Publikováno v: Chemical science [Chem Sci] 2024 Jun 26; Vol. 15 (32), pp. 12861-12878. Date of Electronic Publication: 2024 Jun 26 (Print Publication: 2024).

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.

Autor: Glasser E; Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA., Maji D; Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA., Biancon G; Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA., Puthenpeedikakkal AMK; Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA., Cavender CE; Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA., Tebaldi T; Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy., Jenkins JL; Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA., Mathews DH; Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA., Halene S; Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA., Kielkopf CL; Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.; Wilmot Cancer Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2022 May 20; Vol. 50 (9), pp. 5299-5312.

Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove.

Autor: Chavali SS; Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States., Cavender CE; Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States., Mathews DH; Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States., Wedekind JE; Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States.

Publikováno v: Journal of the American Chemical Society [J Am Chem Soc] 2020 Nov 25; Vol. 142 (47), pp. 19835-19839. Date of Electronic Publication: 2020 Nov 10.

Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.

Autor: Belashov IA; Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA., Crawford DW; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA., Cavender CE; Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA., Dai P; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Beardslee PC; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA., Mathews DH; Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA., Pentelute BL; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA., McNaughton BR; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.; Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA., Wedekind JE; Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2018 Jul 27; Vol. 46 (13), pp. 6401-6415.

Method for the determination of trajectory angles of directional secretory vesicles in cultured astrocytes.

Autor: Cavender CE; Department of Neurobiology, University of Alabama at Birmingham., Gottipati MK; Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham., Malarkey EB; Department of Biotechnology, University of Rijeka, Rijeka, Croatia., Parpura V

Publikováno v: Inquiro [Inquiro] 2013; Vol. 7, pp. 48-52.