Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins.

Abstract

The frontiers of protein design lie in the construction of amino acid sequences and the incorporation of specific motifs, such as binding sites, into receptors, ion channels, or other proteins. This approach allows the production of protein variants with specific functions and purposes. An exemplary application of these bioinformatics resources is the improvement of antimicrobial peptides (AMPs) or the design of synthetic AMPs. This development is significant because of the recent increase in emerging diseases, often caused by pathogens that are difficult to eradicate and exhibit antibiotic resistance. The consequences of this trend include the global extinction of animal species and human deaths. The rapid synthesis of novel and effective AMPs is, therefore, essential. These servers and programs can facilitate the rapid development of vaccines, AMPs, or effective treatments against these pathogens. The aim of this work was to present and propose a procedure for protein construction from sequences and to elucidate the process of using different tools to build these molecules step by step.