Figure 1: Molecular models of a protein(1HIA). (a) The van der Waals surface model (693 atoms); (b) An initial triangulated solvent excluded surface (SES) model (27480 triangles); (c) The decimated triangulated SES model(7770 triangles); (d) Our algebraic spline molecular surface model (7770 patches) generated from (c). 1

The geometry of the polypeptide exit tunnel has been determined using the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The tunnel is a component of a much larger, interconnected system of channels accessible to solvent that permeates the subunit and is connected to the exterior at many points. Since water and other small molecules can diffuse into and out of the tunnel along many different trajectories, the large subunit cannot be part of the seal that keeps ions from passing through the ribosome-translocon complex. The structure referred to as the tunnel is the only passage in the solvent channel system that is both large enough to accommodate nascent peptides, and that traverses the particle. For objects of that size, it is effectively an unbranched tube connecting the peptidyl transferase center of the large subunit and the site where nascent peptides emerge. At no point is the tunnel big enough to accommodate folded polypeptides larger than α-helices.

The previous methods to compute smooth molecular surface assumed that each atom in a molecule has a fixed position without thermal motion or uncertainty. In real world, the position of an atom in a molecule is fuzzy because of its uncertainty in protein structure determination and thermal energy of the atom. In this paper, we propose a method to compute smooth molecular surface for fuzzy atoms. The Gaussian distribution is used for modeling the fuzziness of each atom, and a p-probability sphere is computed for each atom with a certain confidence level. The smooth molecular surface with fuzzy atoms is computed e#ciently from extended-radius p-probability spheres. We have implemented a program for visualizing three-dimensional molecular structures including the smooth molecular surface with fuzzy atoms using multi-layered transparent surfaces, where the surface of each layer has a di#erent confidence level and the transparency associated with the confidence level.

and amino acid sequence

Numerous experimental data on the human peripheral taste system suggest the existence of multiple low-affinity and low-specificity receptor sites which are responsible for the detection and the complete discrimination of a very large number of organic molecules. According to this hypothesis, a given molecule interacts with numerous taste receptors and vice versa. Statistical analysis of taste intensities estimated by 58 human subjects for various molecules enables the calculation of taste intermolecular distances. For the present modeling study, we hypothesized that a short taste distance (i.e. taste similarity) between two distinct molecules indicates that they bind with similar distributions of affinities to the taste receptors, and hence display similar binding motifs. In order to find common molecular binding motifs among 14 selected organic tastants, hydrogen-bonding and hydrophobic interaction properties were mapped onto their molecular surfaces. The 14 surfaces were then cut in 240 fragments, most of which were made up of 2-4 potentially interacting zones. A correspondence index was defined to measure the analogy between two optimally superimposed fragments. The 75 most representative fragments were all matched pairwise. Twelve distinct clusters of fragments were isolated from the 2775 calculated comparisons. These 12 fragment types were used to calculate structural similarity distances. We then performed a combinatorial analysis to identify which fragment combination best reconciled structural and taste distances. We finally identified an optimal subset of seven fragment types out of

this paper (i.e. standard volumes of buried atoms in proteins), and some explanations of Voronoi polyhedra in hypertext form. These items can be retrieved by sending

this document were produced directly from this program

In recent years an effort has been made to supplement traditional methods for drug discovery by computer-assisted "structure-based design." The structure-based approach involves (among other issues) reasoning about the geometry of drug molecules (or ligands) and about the different spatial conformations that these molecules can attain. This is a prehminary report on a set of tools that we are devising to assist the chemist in the drug design process. We describe our work on the fol- lowing three topics: (i) geometric data structures for representing and manipulating molecules; (ii) conformational analysis--searching for lowenergy conformations; and (iii) pharmacophore identification--searching for common features among different hgands that exhibit similar activity.

upported by an analysis of the overall unbinding profile and the magnitude of the mean force, which are similar to those of the unbinding force (i.e. the external force due to the time-dependent perturbation) averaged over several unbinding events. The multiple simulations show that unbinding proceeds along a rather well-defined pathway for a broad range of effective pulling speeds. Initially, there is a distortion of the protein localized in the C-terminal region followed by the fluorescein exit from the binding site. This occurs in steps that involve breaking of specific electrostatic and van der Waals interactions. It appears that the simulations do not explore the same barriers as those measured in the AFM experiments because of the much higher unfolding speed in the former. The dependence of the force on the logarithm of the loading rate is linear and the slope is higher than in the AFM, in agreement with experiment in other systems, where different slopes were observed for diffe

doi:10.1093/nar/gkq395 3V: cavity, channel and cleft volume calculator and extractor