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Graph theory-based simulation tools for protein structure networks
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DOI：10.1016/j.simpat.2022.102640.png)
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Analysis of interactions in biological systems is at the core of almost every biological study. Being a principal tool, graph theory as a mathematical formalism, aims to model relationships and interactions between objects, assisting in the analysis of biological interaction networks at various scales. Over the course of the past few decades, many applications of graph theory to biology have been proposed and developed. In this work, a review of openly available online, graph theory-based tools with biological applications is presented. The selection of tools was based on a structured online search, with a focus on tools that could be utilized to analyze residue interaction and protein-protein interaction networks. After exploring the main features of each tool and with the aim of identifying their use cases in current research, selected papers recent to the extent as possible, referencing the tools, were reviewed with the aim of giving prominence to the effectiveness of graph theory. The latter is of crucial importance upon designing new drug molecules capable of recognizing and modulating the function of proteins (receptors) involved in disease pathophysiology. The knowledge extracted from these tools can be further exploited into cheminformatics approaches and computer-aided new drug discovery techniques. The selected work and specific examples of successful applications were analyzed, in order to highlight how each tool can be integrated in the workflow of different types of studies and to assess to what extent graph theory-based tools can be a valuable ally in the analysis of residue and protein interactions. Moreover, therapeutic development efforts provide further valuable insights and feedback in a plethora of scientific fields like biology, pharmacology and medicine and assist in the further development of graph-theory-based simulation tools for protein structure networks.
Keyword:
Biological networks
Graph theory
Visualization
Simulation
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4.6
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2.6K
被引数:
4.8K
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