Computational Molecular Biology 2024, Vol.14, No.5, 182-190 http://bioscipublisher.com/index.php/cmb 184 understanding the structural basis of PPIs (Dobson, 2019). Additionally, computational methods like molecular dynamics (MD) simulations and docking studies have provided deeper insights into the dynamic nature of these interactions, especially in crowded cellular environments where weak interactions play a significant role (Corrales‐Guerrero et al., 2023). 3.2 Protein-nucleic acid interactions Protein-nucleic acid interactions are critical for processes such as DNA replication, transcription, and repair. Biophysical techniques like X-ray crystallography and NMR spectroscopy have been pivotal in determining the structures of protein-DNA and protein-RNA complexes, revealing the molecular mechanisms of these interactions. Advanced methods such as single-molecule spectroscopy and surface plasmon resonance (SPR) have further enhanced our ability to study these interactions in real-time, providing valuable kinetic and thermodynamic data (Biswas, 2018). 3.3 Protein-ligand interactions Understanding protein-ligand interactions is crucial for drug discovery and the development of therapeutic strategies. Biophysical methods such as isothermal titration calorimetry (ITC), differential scanning fluorimetry (DSF), and SPR are widely used to quantify the binding affinities and kinetics of protein-ligand interactions. MD simulations have also become a powerful tool in this field, offering detailed insights into the binding mechanisms and helping to predict binding free energies accurately (Arcon et al., 2017; Liu et al., 2018). These techniques have been successfully applied to study the interactions between proteins and various ligands, including small molecules, peptides, and other proteins (Figure 1), thereby facilitating the design of more effective drugs. Figure 1 Steps required to conduct an in silico study of food peptides (ligand) and proteins (receptor) (Adopted from Vidal-Limon et al., 2022)
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