The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

Several techniques for the analysis of the internal motions of proteins are available—
separating large collective motions from small, presumably uninteresting motions. Such …

Docking of the 5CITEP inhibitor to snapshots of a 2 ns HIV-1 integrase MD trajectory
indicated a previously uncharacterized trench adjacent to the active site that intermittently …

The need to account for the dynamic behavior of a receptor has long been recognized as a
complicating factor in computational drug design. The use of a single, rigid protein structure …

We present the first receptor-based pharmacophore model for HIV-1 integrase. The
development of “dynamic” pharmacophore models is a new method that accounts for the …

Integration of retroviral cDNA into the host cell chromosome is an essential step in its
replication. This process is catalyzed by the retroviral integrase protein, which is conserved …

Ensemble based virtual screening refers to the use of conformational ensembles from crystal
structures, NMR studies or molecular dynamics simulations. It has gained greater …

Diketo acids such as S-1360 (1A) and L-731,988 (2) are potent and selective inhibitors of
HIV-1 integrase (IN). A plethora of diketo acid-containing compounds have been claimed in …

Publisher Summary This chapter discusses the need for multivariate analysis in biophysical
studies, presents the way principal components analysis (PCA) can be implemented in the …

We have recently presented a new pharmacophore design method that allows for the
incorporation of the inherent flexibility of a target active site. The flexibility of the enzymatic …