Biomedical subjects

B S Duncan

Publications and source records attributed to B S Duncan.

6 recordsLinked to original sources

PubMed1995

Texture mapping parametric molecular surfaces.

Texture mapping is an increasingly popular technique in molecular modeling. It is particularly effective in representing high-resolution surface detail using a low-resolution polygonal model. We describe how texture mapping can be used with parametric molecular surfaces represented as expansions of spherical harmonic functions. We define analytically the texture image and its transformation to a parametric surface. Unlike most methods of texture mapping, this transformation defines a one-to-one correspondence between the surface and the texture; texture coordinates are derived from the location of the surface point and not from physical properties at the surface point. This has advantages for the interactive visualization of surface data. We control the interactive response time by lowering the resolution of the polygon mesh while retaining the high-resolution detail of the texture, or we can lower the resolution of the texture image with the same polygonal model. By using a well-defined convention for texture coordinates, we can use the same image for the original surface or its parametric representation, and we can rapidly switch between images that represent different surface properties without recomputing the texture coordinates. Parametric surfaces allow new flexibility for the visualization of molecular surface data.

Aprotinin↗

PubMed1995

Approximation and visualization of large-scale motion of protein surfaces.

We present a method for the approximation and real-time visualization of large-scale motion of protein surfaces. A molecular surface is represented by an expansion of spherical harmonic functions, and the motion of protein atoms around their equilibrium positions is computed by normal mode analysis. The motion of the surface is approximated by projecting the normal mode vectors of the solvent-accessible atoms to the spherical harmonic representation of the molecular surface. These surface motion vectors are represented by a separate spherical harmonic expansion. Representing the surface geometry and the surface motion vectors by spherical harmonic expansions allows variable-resolution analysis and real-time display of the large-scale surface motion. This technique has been applied to interactive visualization, interactive surface manipulation, and animation.

Computer Graphics↗

PubMed1995

Biomolecular visualization using AVS.

Dataflow systems for scientific visualization are becoming increasingly sophisticated in their architecture and functionality. AVS, from Advanced Visual Systems Inc., is a powerful dataflow environment that has been applied to many computation and visualization tasks. An important, yet complex, application area is molecular modeling and biomolecular visualization. Problems in biomolecular visualization tax the capability of dataflow systems because of the diversity of operations that are required and because many operations do not fit neatly into the dataflow paradigm. Here we describe visualization strategies and auxiliary programs developed to enhance the applicability of AVS for molecular modelling. Our visualization strategy is to use general-purpose AVS modules and a small number of chemistry-specific modules. We have developed methods to control AVS using AVS-tool, a programmable interface to the AVS Command Line Interpreter (CLI), and have also developed NAB, a C-like language for writing AVS modules that has extensions for operating on proteins and nucleic acids. This strategy provides a flexible and extensible framework for a wide variety of molecular modeling tasks.

Artificial Intelligence↗

PubMed1993

Approximation and characterization of molecular surfaces.

The representation and characterization of molecular surfaces are important in many areas of molecular modeling. Parametric representations of protein molecular surfaces are a compact way to describe a surface, and are useful for the evaluation of surface properties such as the normal vector, principal curvatures, and principal curvature directions. Simplified representations of molecular surfaces are useful for efficient rendering and for the display of large-scale surface features. Several techniques for representing surfaces by expansions of spherical harmonic functions have been reported, but these techniques require that the radius function is single valued, that is, each ray from an origin inside the surface intersects the surface at one and only one point. A new technique is described that removes this limitation and can be used to compute surface shape properties.

Chemical Phenomena↗

PubMed1993

Shape analysis of molecular surfaces.

The description of molecular shape is important in the analysis of protein-protein and protein-ligand interactions. We describe volumetric and surface-based techniques for computing shape properties of molecular surfaces. The surface is defined as an isocontour of an approximate electron density function. Each technique can compute several scalar and vector surface properties such as the Gaussian and mean curvature, principal curvatures, and principal curvature directions. Shape properties are derived from the eigenvalues and eigenvectors of a 3 by 3 matrix for each surface point. In the volumetric approach, the matrix is the second derivative of an approximate electron density function. In the surface-based approach, the matrix is the approximate gradient of the surface normal. Derivatives are computed by convolving the density or the surface normals with the derivatives of a Gaussian function. The variance of the Gaussian determines the effective length scale at which the surface is analyzed. Scalar surface properties are displayed as colored dots or shaded triangles, and vector properties are displayed as line segments from each surface point. This report describes the implementation of these procedures and their use in computing the shape properties of Cu-Zu superoxide dismutase.

Computer Simulation↗

PubMed1988

Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562.

A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent computational intractability of this approach is reduced by assembling the protein in pieces, by considering the protein at several levels of abstraction, by utilizing constraint satisfaction methods to consider only a few atoms at a time, and by utilizing artificial intelligence methods of heuristic control to decide which actions will exclude the most conformations. Example results are presented for simulated NMR data from the known crystal structure of cytochrome b562 (103 residues). For 10 sample backbones an average root-mean-square deviation from the crystal of 4.1 A was found for all alpha-carbon atoms and 2.8 A for helix alpha-carbons alone. The 10 backbones define the family of all structures compatible with the data and provide nearly correct starting structures for adjustment by any of the current structure determination methods.

Computer Systems↗