The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the p...

We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha–helices and beta– sheets). This model is based on the following two main ideas. First, we model backbone parts of amino acid residues in a peptide chain by edges in the cubic lattice which are not parallel to the coordinate axes. Second, we describe possible contacts of amino ac...

We introduce a simple theoretical approach for an equilibrium study of proteins with known native-state structures. We test our approach with results on well-studied globular proteins, chymotrypsin inhibitor (2ci2), barnase, and the alpha spectrin SH3 domain, and present evidence for a hierarchical onset of order on lowering the temperature with significant organization at the local level even ...

Several methods have been developed and published over the past years to generate sets of diverse and pharmacologically relevant conformations which can be used within 3D pharmacophore search protocols to increase the number of meaningful hits of such experiments. This review gives some insights into the general challenges and problems in the area of 3D structure and conformation generation and...

body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (i). 348 mhz 1h nmr spectra of (i) have been investigated over the temperature range of 25° to -160°c. two conformation processes affect the 1h nmr spectrum of (i). iterative force-field calculations on the conformations and conformational interconversion paths of (i) give results consisten...

13 Proteins must move between different conformations of their native ensemble to perform their 14 functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this 15 heterogeneity as a spatial and temporal conformational average. Although movement between natively 16 populated alternative conformations can be critical for characterizing molecular mechanisms, it i...

Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separati...

Crystal structures of acetylcholinesterase complexed with ligands are compared with side-chain conformations accessed by native acetylcholinesterase in molecular dynamics (MD) simulations. Several crystallographic conformations of a key residue in a specific binding site are accessed in a simulation of native acetylcholinesterase, although not seen in rotomer plots. Conformational changes upon ...

Ab initio calculations on di-, tri-, tetra-, and pentapeptides of glycine in various conformations are reported. Hydrogen bonding is observed as an important stabilizing force in alpha-helical conformations. These studies on polypeptides of glycine of reasonable size show for the first time that the forces acting to stabilize polypeptide conformations can be extracted directly from theoretical ...

The crystal structures of an inorganic butane analogue, NH(3)BH(2)NH(2)BH(3) (DDAB), were determined using single crystal X-ray diffraction, revealing both anti and gauche conformations. The anti conformation is stabilized by intermolecular dihydrogen bonds in the crystal whereas two gauche conformations of DDAB observed in its 18-crown-6 adducts are stabilized by an intramolecular dihydrogen b...