Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations Rafael Pineda-Alemán 1, Camila Cabarcas-Herrera 2, Antistio Alviz-Amador 3, Humberto Pérez-Gonzalez 1, Erika Rodríguez-Cavallo 2, Darío Méndez-Cuadro 1
1Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, 2Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, 3Pharmacology and Therapeutics Research Group, University of Cartagena
Here, we describe a protocol for the optimization and parameterization of amino acid residues modified with reactive carbonyl species, adaptable to protein systems. The protocol steps include structure design and optimization, charge assignments, parameter construction, and preparation of protein systems.
