A5012013311- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Gastric Cancer Management and Outcomes
- Systemic Lupus Erythematosus Research
- Ubiquitin and proteasome pathways
- Animal Genetics and Reproduction
- Biliary and Gastrointestinal Fistulas
- Bacterial Genetics and Biotechnology
- Diabetes and associated disorders
- CRISPR and Genetic Engineering
- T-cell and B-cell Immunology
- Digestive system and related health
- Colorectal Cancer Surgical Treatments
- Carcinogens and Genotoxicity Assessment
University of Washington
2023-2024
University of Minnesota
1980
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids DNA bases with an atomic all other groups model assemblies that contain proteins, nucleic acids, small molecules, metals, covalent modifications, given their sequences chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion...
Abstract Protein–RNA and protein–DNA complexes play critical roles in biology. Despite considerable recent advances protein structure prediction, the prediction of structures protein–nucleic acid without homology to known is a largely unsolved problem. Here we extend RoseTTAFold machine learning protein-structure-prediction approach additionally predict nucleic complexes. We develop single trained network, RoseTTAFoldNA, that rapidly produces three-dimensional models with confidence...
Abstract Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, there has been considerable interest the engineering of DBPs with new or altered specificities for genome editing other applications. While some success reprogramming naturally occurring using selection methods, computational design that recognize arbitrary target sites remains an outstanding challenge. We describe a method small specific sequences through interactions bases major groove,...
In a recent paper, Thomson & Bodmer (1979) explored several conceptual and analytic issues involved in studying the association of HLA haplotypes with disease. One key problem they emphasized was assessment statistical significance third order linkage disequilibrium between two genes disease susceptibility gene. We have formulated an approach to this illustrate by deriving such tests true haplotype associations for models previously studied Terasaki Mickey (1975) (1977). A numerical...