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In a first step toward the development of an efficient and accurate protocol to estimate amino acids' pKa's in proteins, we present in this work how to reproduce the pKa's of alcohol and thiol based residues (namely tyrosine, serine, and cysteine) in aqueous solution from the knowledge of the experimental pKa's of phenols, alcohols, and thiols. Our protocol(More)
New developments in the field of theoretical chemistry require the computation of numerous Molecular Potential Energy Surfaces (PESs) to generate adequate quantum force field parameters. Because workstations alone cannot fulfill the requirements of these modern chemical advances, we present in this paper how we have tackled this problem using several(More)
Deamidation reaction in pentapeptides and the enzyme Trio-sephosphate isomerase (TPI) is investigated by molecular dynamics. For TPI, simulations based on classical AMBER force field are performed in 60 to 90 ns timescale for six distinct samples. Conformational changes, desolvation effects, and hydrogen bond networks are analyzed to interpret the(More)
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