A5038486947- Protein Structure and Dynamics
- DNA and Biological Computing
- Machine Learning in Bioinformatics
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- Protein Degradation and Inhibitors
- Graph Theory and Algorithms
Toshiba (Japan)
2024
Tokyo Institute of Technology
2021-2022
In the polyomino puzzle, aim is to fill a finite space using several pieces with no overlaps or blanks. Because it an NP-complete combinatorial optimization problem, various probabilistic and approximated approaches have been applied find solutions. Several previous studies embedded puzzle in QUBO where original objective function constraints are transformed into Hamiltonian of simulated Ising model. A solution obtained by searching for ground state simulating dynamics multiple-spin system....
Protein–ligand docking plays a significant role in structure-based drug discovery. This methodology aims to estimate the binding mode and free energy between drug-targeted protein candidate chemical compounds, utilizing tertiary structure information. Reformulation of this as quadratic unconstrained binary optimization (QUBO) problem obtain solutions via quantum annealing has been attempted. However, previous studies did not consider internal degrees freedom compound that is mandatory...
Metagenomic analysis, a technique used to comprehensively analyze microorganisms present in the environment, requires performing high-precision homology searches on large amounts of sequencing data, size which has increased dramatically with development next-generation sequencing. NCBI BLAST is most widely software for searches, but its speed insufficient throughput current DNA sequencers. In this paper, we propose new, high-performance search algorithm that employs two-step seed strategy...