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Software Package for Molecular Modelling and Structural Characterization

IP.com Disclosure Number: IPCOM000038550D
Original Publication Date: 1987-Feb-01
Included in the Prior Art Database: 2005-Jan-31
Document File: 3 page(s) / 14K

Publishing Venue

IBM

Related People

Pickover, CA: AUTHOR

Abstract

The difficulty in comparing complicated molecular structures and phenomena motivates the development of these software packages, systems, and methods. The highly interactive nature of their user interfaces and the variety of data representations available to the user suggest the extension of these analyses beyond the biomolecular domain. A set of software is disclosed which facilitates the structural and dynamical characterization of biomolecules (or other large molecules). The various routines currently run on an IBM 3277 GA and Tektronix Graphics display. The support software is PL/I, and the interactive graphics language is GCS. The Random-Dot Display Program makes use of a moire interference pattern to allow researchers to compare orientations of structural parts, such as protein subunits.

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Software Package for Molecular Modelling and Structural Characterization

The difficulty in comparing complicated molecular structures and phenomena motivates the development of these software packages, systems, and methods. The highly interactive nature of their user interfaces and the variety of data representations available to the user suggest the extension of these analyses beyond the biomolecular domain. A set of software is disclosed which facilitates the structural and dynamical characterization of biomolecules (or other large molecules). The various routines currently run on an IBM 3277 GA and Tektronix Graphics display. The support software is PL/I, and the interactive graphics language is GCS. The Random-Dot Display Program makes use of a moire interference pattern to allow researchers to compare orientations of structural parts, such as protein subunits. Method: If a pattern of random dots is superimposed on itself and rotated by a small angle, concentric circles are perceived about the point of rotation. If the angle of rotation is increased, the perceived circles gradually disappear until a totally unstructured dot display is seen. This effect demonstrates the ability of the human visual system to detect local autocorrelations and may suggest a physiological basis of form perception in higher animals. Demonstration: This graphical technique may be used in situations where two conformers of a lobed molecule are known and an equivalent axis of rotation relating the two is desired. First, two identical random- dot patterns are superimposed over the computer graphics representation of one form of the protein. One of the dot patterns is rotated along with one lobe until the lobe is in its new position, while the other remains with the stationary lobe. Even a small change, represented by a one-degree rotation of one lobe relative to the other, creates a figure where the axis of rotation can begin to be perceived at the center of the concentric circles. DNA Spectrogram and Power Spectra - Two useful ways of describing base content and periodicity for nucleic acid sequences are the spectrogram and three-dimensional power spectrum, representations similar to those frequently used in the field of digital signal processing. The user assigns a numerical value to each of the DNA bases (G,C,A,T), thereby converting the string of characters to a digitized waveform. The user also specifies a data window (i.e., how many contiguous bases will be characterized in each strip of the output display) and a window overlap (how many bases the adjacent windows have in common). If the user desires to focus on smaller regions of the DNA and is not concerned with low frequency patterns, a small window may be chosen. If the user desires a more global characterization of the patterns within the DNA sequence, a large window is chosen. The overlap parameter makes it easier to capture the spatial dynamics of the features of interest. In both the 3-D p...