Showing papers in "Journal of Molecular Graphics in 1992"

TL;DR: The program SCARECROW has been developed to help the molecular modeler to analyze and display the very big and complex data files produced by molecular dynamics programs.

TL;DR: A new interactive graphics program is described that provides a quick and simple procedure for identifying, displaying, and manipulating the indentations, cavities, or holes in a known protein structure.

TL;DR: A new modeling program, BUILDER, that combines database searching techniques and structure generation algorithms within an interactive graphics modeling environment (MidasPlus) and its ability to produce novel structures is described.

TL;DR: The method is based on a Monte Carlo algorithm applied to the translational and rotational degrees of freedom of the probe fragment and could consistently reproduce the complex found in the crystal structure searching from random initial positions in cubes about the binding site.

TL;DR: Flexible computer program that allows the analysis and display of molecular coordinates from crystallography, NMR, and molecular dynamics, and can also display two-dimensional and three-dimensional data using many graph types.

TL;DR: Two new similarity indices are suggested that calculate the electrostatic potential similarity using a difference-based numerator, and the form of the new indices allows the creation of additional software functions that enhance the flexibility of similarity calculations and permit thecreation of similarity maps.

TL;DR: The method uses a pattern-recognition technique based on cellular logic operations to distinguish between convex and concave regions of a protein and solid fills protein cavities and automatically defines a boundary between cavity and exterior free space.

TL;DR: Three new routines (LOCK, KEY and LOCKSMITH) for the program HINT (hydrophobic interactions) are described and demonstrated and many hydropathic features of the "ideal" drug predicted by the KEY map overlap with actual structural Features of the most active hemoglobin allosteric modifiers.

TL;DR: It is shown that pharmacophoric pattern searches of databases of flexible 3D molecules represented in this way can be carried out using screen and geometric searching algorithms that are analogous to those used for searching databases of rigid 3D structures.

TL;DR: From two chosen sections, a methodology of generating the optimal matching of two shapes is established, and this efficient method could be used as a preprocessing for a tridimensional shape complementarity approach between two molecular surfaces.

TL;DR: A new algorithm for creating diverse, irregular and physically reasonable three-dimensional linear atomic chains is described, which could serve as useful structural templates for joining up regions in an active site where a ligand might interact strongly with the receptor.

TL;DR: In this article, a statistical measure of polypeptide conformational behavior for substructures in a defined structural context from a library of highly refined protein structures is presented. But the program is limited to the reconstruction of a complete set of three-dimensional protein coordinates from α-carbon coordinates.

TL;DR: Two-dimensional image processing techniques are used to create black and white illustrations from conventional z-buffer images that have the advantage of faithful reproduction in publication and ease of display on workstations and laser printers.

TL;DR: FOCUS is a program for analyzing molecular dynamics simulations that utilizes novel methods based on digital signal-processing techniques to characterize the various motions and extracts "characteristic modes" and associated frequencies.

TL;DR: A programming language OCL (Object Command Language) is written to solve two recurring problems that arise during the construction of molecular models and during the geometrical characterization of macromolecule: how to move precisely and reproducibly any part of a molecular model in any user-defined local reference axes.

TL;DR: A three-dimensional model for the complex between human serum retinol binding protein and transthyretin (formerly named prealbumin) is presented by interactive rigid-body computer graphics docking and the characterization of the molecular surfaces in terms of fractal dimension.

TL;DR: A novel predictive method is presented here, which attempts to address some of the shortfalls inherent in representing a protein as a simple text-like sequence of amino acids, by deriving pattern-matching data from the predicted physical properties of a protein chain rather than from the sequence itself.

TL;DR: The system presented is special in its focus on the fast characterization of the progression of sequence data using a graphics supercomputer with several controlling parameters.

TL;DR: The energetics of solvent-atom and atom-atom nonbonded interactions can be described, for protein structures, in terms of the accessible and the contact atomic surface areas, respectively, which allows one to visualize the spatial extent and distribution of these interactions.

TL;DR: Results suggest that the unusual catalytic network observed in the studied PLA2 is a structural feature of the protein and not a crystal artifact.

TL;DR: A software system has been developed for facilitating modeling calculations on large numbers of molecules and can be used to perform a succession of calculations aimed at identifying the major low-energy conformers of each of a set of molecules, starting only from their chemical connectivities.

TL;DR: To obtain better insights into the dynamic nature of hydrogen bonding, computer graphics representations were introduced as an aid for the analysis of molecular dynamics trajectories to reflect the frequency and the type of hydrogenonding occurring during the simulation period.

TL;DR: Results of the investigations reveal that the isothiourea moiety of dimaprit most probably interacts with the histamine H2-receptor through the sulphur and nitrogen atom, the first atom acting as a proton acceptor and the second one as aProton donor.

TL;DR: A PC version of three-dimensional molecular graphics package has been developed to run under MS-DOS environment on IBM PC-compatible computers equipped with a VGA graphics board.

TL;DR: A new version of the molecular graphics program FRODO was developed to allow the range of Tektronix graphics stations to be used for molecular modeling and crystallographic applications.