The work in this dissertation explores the use of massive computational power available
through modern supercomputers as a virtual laboratory to aid drug discovery. As of …

The dynamic character of proteins strongly influences biomolecular recognition
mechanisms. With the development of the main models of ligand recognition (lock-and-key …

Figure 3.1 MD simulation showing the change of conformational equilibria perturbing the
interactions between the motor domain and the converter domain due to a single mutation …

Drug design through computer, a re Drug Design (CADD) technologies benefit of the CADD
is cost effectiv are used in CADD. There are differe energy minimization molecular do …

Rapid advances in scientific research have led to unprecedented data deluge and
significant challenges in data interoperability, certification and collaboration. The …

The accurate prediction of biomolecular recognition is fundamental to modern drug
discovery. Computational chemists seek to optimize interactions between proteins and drug …

Aspartic proteases are a family of protease enzymes that utilize two aspartate residues to
catalyze the hydrolysis of their peptide substrates. Many aspartic-protease-family members …

Slow-onset inhibition is observed for many successful drugs on the market presumably since
this leads to a better pharmacodynamic profile. However, the structural basis for slow-onset …

Since acquired immune deficiency syndrome (AIDS) was recognized by the US centers for
disease control and prevention in 1981 (Gallo, 2006), a large number of patients have died …

Conformational changes in biomolecules often take place on longer timescales than are
easily accessible with unbiased molecular dynamics simulations, necessitating the use of …