Showing papers in "Journal of Molecular Graphics in 1995"

TL;DR: The SURFNET program generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file, and can generate 3D contour surfaces of the density distributions of any set of 3D data points.

TL;DR: The program reads ASCII format structure files including PDB, plot files from the graphics programs O and FRODO, and Cartesian coordinates from ChemDraw 3D, and has a graphical interface that features floating button palettes for objects and tools.

TL;DR: A computational method is presented for probing geometric, topological, and structural characteristics of one-dimensional tunnel structures in solid inclusion compounds in urea and thiourea inclusion compounds.

TL;DR: This program, originally developed to facilitate the protein sequence analysis coupled with multiple alignments and predicted secondary structures of proteins, now comprises a powerful 3D module to display and handle macromolecular structures.

TL;DR: A computer-assisted docking of QHS with hemin from various starting configurations and found that, in the most stable docked configuration, the endoperoxide bridge is in close proximity to the hemin iron.

TL;DR: A user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes, is presented.

TL;DR: A digital method based on mathematical morphological operations to obtain three types of surfaces: van der Waals surface, solvent-accessible surface, and molecular surface, to extract cavities on the surface and interior part of the molecule and to extract the ligand portions in contact with the cavities.

TL;DR: A tabular representation of protein folding patterns is described, which comprises information about the order along the chain of helices and strands of sheet, identifies the elements of secondary structure that interact, and indicates their relative orientation.

TL;DR: XmMol is a desktop tool designed to provide both interactive molecular graphics on X11 displays and easy interface with external applications and communication protocols allow the user to develop new external features or to use it as a visualization tool for external numerical programs.

TL;DR: The protein-folding procedure described in this article consists of two successive steps: a theoretical transition from an ideal alpha helix to an ideal beta sheet is first imposed on the protein conformation, in order to calculate an initial secondary structure, and a new semiempirical equation is derived to calculate the total energy of a macromolecular system including its free energy of solvation.

TL;DR: Techniques that allow for the interactive computation and display of molecular structures and properties are presented and a better understanding of the electronic behavior of the systems can be achieved.

TL;DR: Self-organizing maps generated by Kohonen neural networks provide a method for transforming multidimensional problems into lower dimensional problems and are extended to rank histamine H2 agonists in order of biological activity.

TL;DR: A variety of molecular modeling and molecular orbital techniques was used to find molecular descriptors that could be used to derive an empirical equation to describe the glass transition temperature of two related classes of poly(arylene ether)s.

TL;DR: A method for the approximation and real-time visualization of large-scale motion of protein surfaces by projecting the normal mode vectors of the solvent-accessible atoms to the spherical harmonic representation of the molecular surface.

TL;DR: It is demonstrated that, for a set of dopamine agonists, D1 ligands show higher similarity in this property that D2 analogs, and this indicator of similarity is more successful at accounting for D1 selectivity than previous methods.

TL;DR: This work describes how texture mapping can be used with parametric molecular surfaces represented as expansions of spherical harmonic functions, and defines analytically the texture image and its transformation to a parametric surface.

TL;DR: In the two examples described, namely, a series of benzodiazepine agonists and a set of serotonin 5-HT3 antagonists, the program has been shown to produce useful pharmacophoric overlaps that can be used in the design of novel therapeutic agents.

TL;DR: Two computer models of the outer vestibule of the pore of the N-type voltage-gated Ca2+ channel are predicted and suggest that a ring of threonines and an aspartate might be present between the mouth of thepore and the filter, and hence the models may prove useful in suggesting future mutagenesis experiments.

TL;DR: The process of stereolithography, which automatically fabricates plastic models from designs created in certain computer-aided design programs, has been applied to the production of accurate plastic molecular models, resulting in hard plastic models that accurately represent the computed or experimental input structures.

TL;DR: This work deals with the simpler two-dimensional maps of the entire molecular surface projected onto an MEP-MLP plane and analyzes how these maps change with the following factors: composition and molecular geometry, the quality of the computation of MEP, and the parameter set used for evaluating the lipophilicity potential.

TL;DR: Application of an HME to the prediction of protein secondary structure is shown to provide no advantages over a single network, and various new input representations are tried to incorporate the effect of residues a long distance away in the one-dimensional amino acid chain.

TL;DR: The utility of graphical representations that highlight structural uncertainty are illustrated by the applying PROTEAND to the globin family of proteins, and it is shown that certain types of structural variation are best illustrated with different methods of display.

TL;DR: It is shown that the transport of molecular models over the WWW using VRML is a very efficient and powerful method for the exchange of molecular information.

TL;DR: This paper describes visualization strategies and auxiliary programs developed to enhance the applicability of AVS for molecular modelling and develops NAB, a C-like language for writing AVS modules that has extensions for operating on proteins and nucleic acids.

TL;DR: Using a nonlinear mapping technique, it is demonstrated that proteins folded in two dimensions display the same overall structural features as their three-dimensional counterparts.

TL;DR: Two new approaches are described here are a systematic conformation search running on PCs and a new approach to 3D similarity analysis of lipophilic potentials.

TL;DR: VISTAS is a suite of programs for protein sequence and structure analysis that allows the simultaneous display of multiple sequence alignments, of known or model 3D structures, and of 2D graphic representations of sequence and/or alignment properties.

TL;DR: A model allowing us to predict the affinity of new compounds is constructed, based on simple graphic tools coupled to a cluster significance analysis, and the principal electronic and structural characteristics leading to a selective activity were revealed.

TL;DR: Extensions to the Brookhaven Protein Data Bank file format for incorporating scene information such as viewing parameters, additional molecular information, and user-defined graphics are implemented and proposed for incorporation into visualization programs.

TL;DR: This article describes the integration of programs from the widely used CCP4 macromolecular crystallography package into a modern data flow visualization environment (application visualization system [AVS]), which provides a simple graphical user interface, a visual programming paradigm, and a variety of 1-, 2-, and 3-D data visualization tools for the display of graphical information and the results of crystallographic calculations.