Geometric deep learning of protein-DNA binding specificity.

Autor: Mitra R; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Li J; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Sagendorf JM; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Jiang Y; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Cohen AS; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Chiu TP; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Glasscock CJ; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Rohs R; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. rohs@usc.edu.; Department of Chemistry, University of Southern California, Los Angeles, CA, USA. rohs@usc.edu.; Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA. rohs@usc.edu.; Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA, USA. rohs@usc.edu.

Publikováno v: Nature methods [Nat Methods] 2024 Sep; Vol. 21 (9), pp. 1674-1683. Date of Electronic Publication: 2024 Aug 05.

PNAbind: Structure-based prediction of protein-nucleic acid binding using graph neural networks.

Autor: Sagendorf JM, Mitra R, Huang J, Chen XS, Rohs R

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Mar 02. Date of Electronic Publication: 2024 Mar 02.

Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.

Autor: Lei X; Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: xiaoleiusc@gmail.com., Zhao J; Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA., Sagendorf JM; Quantitative and Computational Biology, Departments of Biological Sciences, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA., Rajashekar N; Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Xu J; Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Dantas Machado AC; Quantitative and Computational Biology, Departments of Biological Sciences, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA., Sen C; Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Rohs R; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; Quantitative and Computational Biology, Departments of Biological Sciences, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA., Feng P; Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA., Chen L; Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: linchen@usc.edu.

Publikováno v: Journal of molecular biology [J Mol Biol] 2020 Sep 04; Vol. 432 (19), pp. 5499-5508. Date of Electronic Publication: 2020 Jul 15.

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.

Autor: Azad RN; Department of Chemistry, Boston University, Boston, MA 02215, USA., Zafiropoulos D; Department of Chemistry, Boston University, Boston, MA 02215, USA., Ober D; Department of Chemistry, Boston University, Boston, MA 02215, USA., Jiang Y; Department of Chemistry, Boston University, Boston, MA 02215, USA., Chiu TP; Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA., Sagendorf JM; Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA., Rohs R; Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA., Tullius TD; Department of Chemistry, Boston University, Boston, MA 02215, USA.; Program in Bioinformatics, Boston University, Boston, MA 02215, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2018 Mar 16; Vol. 46 (5), pp. 2636-2647.

Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site.

Autor: Li J; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.; State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China., Dantas Machado AC; Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.; Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States., Guo M; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China., Sagendorf JM; Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.; Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States., Zhou Z; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China., Jiang L; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China., Chen X; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.; State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China., Wu D; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China., Qu L; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China., Chen Z; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China., Chen L; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.; Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States., Rohs R; Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.; Department of Physics and Astronomy and Department of Computer Science, University of Southern California , Los Angeles, California 90089, United States., Chen Y; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health and Laboratory of Structural Biology, Xiangya Hospital, Central South University , Changsha, Hunan 410008, China.; State Key Laboratory of Medical Genetics and College of Life Science, Central South University , Changsha, Hunan 410008, China.; Collaborative Innovation Center for Cancer Medicine , Guangzhou, Guangdong 510060, China.

Publikováno v: Biochemistry [Biochemistry] 2017 Jul 25; Vol. 56 (29), pp. 3745-3753. Date of Electronic Publication: 2017 Jul 11.