The goal of this article is to reduce the complexity of the side chain search within docking problems. We apply six methods of generating side chain conformers to unbound protein structures and determine their ability of obtaining the bound conformation in small ensembles of conformers. Methods are evaluated in terms of the positions of side chain end groups. Results for 68 protein complexes yi...

Human serum albumin (HSA) is a very important multi-domain transporter protein in the circulatory system responsible for carriage of various kinds of ligands within the physiological system. HSA is also known to undergo conformational transformation at different pH(s) and temperatures. In this report we have studied the binding interactions of a photosensitizing drug, protoporphyrin IX (PPIX) w...

The synthesis of two [4]-dendralene compounds incorporating thiophene-(p-nitrophenyl) donor-acceptor units is presented. The dendralenes adopt two different conformers in solution and solid state and the transformation between the structures can be controlled by light and heat. The electron-donating components of the dendralenes are represented by bromothienyl (in 13) and ethylenedioxythiophene...

Hydrogen abstraction reactions by the methyl radical from n-butanol have been investigated at the ROCBS-QB3 level of theory. Reaction energies and product geometries for the most stable conformer of n-butanol (ROH) have been computed, the reaction energies order α < γ < β < δ < OH. The preference for n-butane to favour H-abstraction at C(β) and C(γ) while, in contrast, n-butanol favours radical...

BACKGROUND Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. RESULTS Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through ...

The laser-induced fluorescence spectrum of jet-cooled L-tyrosine exhibits more than 20 vibronic bands in the 35450-35750 cm(-1) region. We attribute these bands to eight conformers by using results of UV-UV hole-burning spectroscopy. These isomers are classified into four groups; each group consists of two rotational isomers that have a similar side-chain conformation but different orientations...

The first is an examination by Csonka and French of the ability of DFT to predict the relative energy of carbohydrate conformation energies. 1 They examined 15 conformers of αand β-D-allopyranose, fifteen conformations of 3,6-anydro-4-Omethyl-D-galactitol and four conformers of β-D-glucopyranose. The energies were referenced against those obtained at MP2/a-cc-pVTZ(-f)//B3LYP/6-31+G*. (This unus...