2016/02/25 by M. R. Gunner, Gunner, Marilyn R., Nathan Baker +1
Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies
paper · pdf · doi:10.48550/arxiv.1602.07957
openalex publication_date 2016/02/25 · openalex created_date 2022/09/19 · openalex updated_date 2026/07/28
Proteins change their charge state through protonation and redox reactions as\nwell as through binding charged ligands. The free energy of these reactions are\ndominated by solvation and electrostatic energies and modulated by protein\nconformational relaxation in response to the ionization state changes. Although\ncomputational methods for calculating these interactions can provide very\npowerful tools for predicting protein charge states, they include several\ncritical approximations of which users should be aware. This chapter discusses\nthe strengths, weaknesses, and approximations of popular computational methods\nfor predicting charge states and understanding their underlying electrostatic\ninteractions. The goal of this chapter is to inform users about applications\nand potential caveats of these methods as well as outline directions for future\ntheoretical and computational research.\n