PS-GO parametric protein search engine

• Published in: Computational and structural biotechnology journal 2024-12, Vol.23, p.1499-1509
• Main Authors: Mi, Yanlin, Marcu, Stefan-Bogdan, Tabirca, Sabin, Yallapragada, Venkata V.B.
• Format: Article
• Language: English
• Subjects: Parametric protein design; Parametric protein search; Protein parameters database; Protein search engine; Protein topology; Software/Web server
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2024.04.003

With the explosive growth of protein-related data, we are confronted with a critical scientific inquiry: How can we effectively retrieve, compare, and profoundly comprehend these protein structures to maximize the utilization of such data resources? PS-GO, a parametric protein search engine, has been specifically designed and developed to maximize the utilization of the rapidly growing volume of protein-related data. This innovative tool addresses the critical need for effective retrieval, comparison, and deep understanding of protein structures. By integrating computational biology, bioinformatics, and data science, PS-GO is capable of managing large-scale data and accurately predicting and comparing protein structures and functions. The engine is built upon the concept of parametric protein design, a computer-aided method that adjusts and optimizes protein structures and sequences to achieve desired biological functions and structural stability. PS-GO utilizes key parameters such as amino acid sequence, side chain angle, and solvent accessibility, which have a significant influence on protein structure and function. Additionally, PS-GO leverages computable parameters, derived computationally, which are crucial for understanding and predicting protein behavior. The development of PS-GO underscores the potential of parametric protein design in a variety of applications, including enhancing enzyme activity, improving antibody affinity, and designing novel functional proteins. This advancement not only provides a robust theoretical foundation for the field of protein engineering and biotechnology but also offers practical guidelines for future progress in this domain. •PS-GO allows parametric protein retrieval by adjusting key parameters.•With parallel computation, PS-GO swiftly calculates numerous protein parameters.•PS-GO lets users tweak protein sequences, enriching structural diversity.•PS-GO's intuitive interface and NLP tech expand accessibility beyond researchers.