Protein and Protein Interactions

Dear Colleagues,

Proteins play a vital role in sustaining life, requiring the formation of specific 3D structures to manifest their essential biological functions. Life is about relationships between molecules, not a property of any single molecule. Among the pivotal elements contributing to various processes are noncovalent interactions, which include protein-protein, protein-DNA/RNA, ligand-receptor, drug-target, or host-guest interactions. Determining molecular interactions can be achieved through structural and experimental methods like X-ray crystallography, NMR or Cryo-EM techniques. Functional assays, including yeast-two hybrid, pulldown experiment, or FRET method, conducted in laboratory settings, can also provide evidence of these interactions. It remains a formidable challenge to computationally predict these intricate molecular interactions. Physics-based methods for calculating binding free energy and empirical scoring functions for assessing binding affinities have been used to investigate protein-protein interactions. Nevertheless, the lack of a mechanistic understanding of molecular interactions poses a significant obstacle to computationally identify binding partners and to elucidate the corresponding regulatory mechanisms governing their functions.

This Special Issue for IJMS aims at gathering contributions with the focus on improving the mechanistic understanding of protein and protein interactions including ligand and protein interactions using computational approaches. Development of new computational methods or software tools are encouraged.

Dr. Wu Xu
Guest Editor

Manuscript Submission Information

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• protein and protein interactions
• ligand and protein interactions
• computational method
• geometry-based
• energy-based
• conformational changes
• binding site prediction
• structural biology
• computational biology and bioinformatics