2025 · Bioinformatics · Oxford University Press · added 2026-04-21
Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a Show more
Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein question answering systems. To tackle these issues, we propose the Prot2Chat framework. Results: We modified ProteinMPNN to encode protein sequence and structural information in a unified way. We used a large language model Show less
Abstract To assess the nature of the relationship between the integral conformational stability of tetrapeptides and the main types of β-turns (which are also tetrapeptides), spectrum diagrams, the as Show more
Abstract To assess the nature of the relationship between the integral conformational stability of tetrapeptides and the main types of β-turns (which are also tetrapeptides), spectrum diagrams, the asymmetry of the distribution of conformationally stable and unstable tetrapeptides have been calculated. It has been shown that β-turns of types I', II, and II' consist mainly of conformationally labile peptides; this is consistent with the context-predetermined nature of their structure. Since, as we have shown earlier, in this case the conformation is imposed by external conditions (specifically, the closure of the cycle), the prevalence of conformation-labile peptides facilitates the formation of the structure due to external factors. The type I β-turn is an exception, since peptides with different conformational lability are distributed fairly even in it. It can be assumed that the formation of the type I β-turn is not contextually determined. Show less
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent Show more
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value. Show less