The proposed PhD thesis addresses the challenges arising from the explosive growth of sequence and structure databases resulting from recent breakthroughs in next-generation sequencing and structural bioinformatics. The vast amount of biological data presents opportunities for transformative genomics and proteomics analyses, but the bottleneck lies in the efficient handling of these massive datasets within practical time frames. This research aims to develop cutting-edge algorithms and software leveraging the computational power of modern processors and graphics accelerators. The doctoral candidate will focus on creating high-performance solutions for encoding protein and nucleic acid sequences, conducting similarity searches in sequence and structure spaces, performing structure docking, and addressing other large-scale downstream tasks. The outcomes of this study are anticipated to contribute to advancements in several research domains, including structure-based drug discovery, offering novel computational tools for the broader biological research community.