PEPCRE: an interactive program to create,manipulate and display oligopeptides

PEPCRE is an interactive computer graphics program for the rapid construction, manipulation and display of oligopeptides. Essentially any desired conformation of an oligopeptide can be constructed in a simple and straightforward manner. The program provides various display and output possibilities. It is user-friendly and is written in FORTRAN 77 for use on inexpensive, monochrome graphics terminals.     

Computer graphics presentation modes for biologic data. Types and examples

New advances in automated cytology, computer microscopy, densitometry and other instrumentation for feature/scene acquisition or analysis have resulted in higher information densities than heretofore encountered. Two-, three- and four-space computer graphics provide favorable bandwidth conditions for transforming complex, large-scale data sets into visual displays that allow a human observer, utilizing the brain's efficient processing of visual information, to rapidly grasp relationships and synthesize concepts. Examples of multidimensional displays are presented, all developed by neuroscientists who are not computer specialists. Because modern graphics and image-synthesis techniques can now be implemented on any one of several commercially available very-high-speed integrated-circuit-based display systems, at moderate cost, exploitation of specifically visual presentation should be carefully considered in any system generating information in high density.     

Displaying inter-main chain hydrogen bond patterns in proteins

Two computer graphics techniques for displaying hydrogen bonds between the main chains of different proteins are described, and illustrated for two thiol proteases. (The X-ray crystallography was performed by Kamphuis et al. in 1984,¹ and by Baker and Dodson in 1980.²) One is a three-dimensional model that can be manipulated in space; the hydrogen bonds are represented with the smoothed α-carbon plot of the polypeptide chain. In the other type of display, hydrogen bonds are viewed in relation to the one-dimensional sequence. Both types of picture facilitate visualization of hydrogen bond patterns, such that loop motifs, as well as α-helices and β-sheets, can be examined easily. We suggest that such displays are useful as a general means of displaying whole proteins and whole domains because they reveal more information than do conventional simplified pictures of proteins, which focus exclusively on α-helices and β-sheets. These techniques can be implemented on a UNIX-based computer graphics workstation. (UNIX is a trademark of Bell Telephone laboratories.)     

Computer graphics with computerized tomography for functional neurosurgery

A computer graphics technique for computer-assisted stereotactic surgery is presented. The program is designed to aid the surgeon by presenting an on-line graphics display of stereotactic probes and electrodes superimposed on cross sections of the human brain stem. This technique simulates an otherwise blind surgical procedure on a graphics screen for use during surgery. An earlier system based around the DEC MINC-11 BA computer system has been used by the authors for the performance of stereotactic surgery with conventional ventriculography. This system has been upgraded and is now configured about an even more compact microprocessor-based hardware system with expanded graphics capabilities, which also allows its use with computerized tomography.     

Processing of multi-dimensional NMR data with the new software PROSA

Summary The new program PROSA is an efficient implementation of the common data-processing steps for multi-dimensional NMR spectra. PROSA performs linear prediction, digital filtering, Fourier transformation, automatic phase correction, and baseline correction. High efficiency is achieved by avoiding disk storage of intermediate data and by the absence of any graphics display, which enables calculation in the batch mode and facilitates porting PROSA on a variety of different computer systems; including supercomputers. Furthermore, all time-consuming routines are completely vectorized. The elimination of a graphics display was made possible by the use of a new, reliable automatic phase-correction routine. CPU times for complete processing of a typical heteronuclear three-dimensional NMR data set of a protein vary between less than 1 min on a NEC SX3 supercomputer and 40 min on a Sun-4 computer system.     

Interactive computer surface graphic study of the binding of an antibody to the chromatin subunit

The binding of an IgG molecule to a chromatin subunit has been simulated by the interactive computer surface graphics technique. This technique permits the facile display of the surface of macromolecules for which atomic co-ordinates are known. The computer generated projections reveal spatial relationship between the IgG and the nucleosome. Studies of these projections provide insights into the immunogenicity and antigenicity of the chromatin subunit. The concepts discussed are helpful in understanding the manner in which IgG molecules specific to DNA bases, chromosomal proteins, irradiated DNA and to chemical carcinogens bind to the genome.     

A graphical user interface for quantitative imaging and analysis of electrophoretic gels and autoradiograms.

DNA/GUI (DNA Graphical User Interface) is an interactive software system for rapid and efficient analysis of images of the types used in genome mapping, such as autoradiograms and electrophoretic gels. Images are digitized using a commercially available charge-coupled-device (CCD) camera system and analyzed on a graphics workstation using a menu-driven user interface. DNA/GUI features automatic lane and band detection, simultaneous display of multiple images and a unique spatial-normalization algorithm. Images and their associated data are archived and easily available for later recall. Preliminary results indicate that DNA/GUI is a useful tool in the analysis and comparison of images used in a variety of applications such as genetic-linkage analysis and DNA restriction mapping. The interactive display software is based on the X Window System and is therefore readily portable to a variety of graphics workstations.     

A multimodal system for reconstruction and quantification of neurologic structures

The utility of computers and computer graphics as aids in the study of nervous system architecture is growing. However, modern histologic, immunocytologic and biochemical methods for revealing the underlying microarchitecture and macroarchitecture of the nervous system yield data formats requiring disparate computer acquisition, analysis and display approaches, capable of spanning many orders of magnitude of scale. This paper describes the Image Graphics Laboratory data acquisition, processing and display system, whose various components and programs may be used singly or in concert to enable definition of various tissue properties at different levels of resolution and integration. Examples are given of the system's use in light microscopic two-dimensional and three-dimensional reconstructions, autoradiographic reconstructions, reconstructions from projected images, reconstructions of impregnated cells (e.g., whole neurons) and peripheral nerve image analysis.     

Generating precise mechanical stimuli and recording chordotonal organ discharge patterns using a microcomputer

A computer-controlled system for the investigation of the responseproperties of the tibio-femoral chordotonal organ in the locustis described. The computer is used to generate small amplitudesinusoidal movements of the tibia via a small servo-controlledmotor. The resulting response recorded via a suction electrodeis simultaneously detected, processed and stored on disk. Fullconstructional details for all hardware required are given.The software, developed for a BBC microcomputer, in additionto controlling all the hardware, has graphics and analysis routinesenabling the operator to display and manipulate the stored data.     

An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.

This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is displayed on a simple graphics terminal. Use of a graphics terminal allows the user to display the whole of the two sequences in one screenful or to home-in on regions of interest to examine them in more detail. The program is interactive and so the user can easily see the effect of changes to variables and can use inbuilt editing functions to make insertions to produce alignments of the two sequences. These aligned sequences can then be saved on disk files for further processing.     

PCDRA: PC interactive molecular representation and modeling system

PCDRA was designed to provide the average biologist with a user-friendly molecular display on a low-cost personal computer. The package is menu driven and is built so that a biologist, with tittle or no computing knowledge, finds it easy to use. The system gives a color representation with depth cueing of a protein whose atomic coordinates are stored as a PDB file. Moreover, the system presents several features similar to HYDRA¹ and therefore is a good introduction to molecular graphics, especially for beginners in protein modeling.     

Enabling High Grayscale Resolution Displays and Accurate Response Time Measurements on Conventional Computers

Display systems based on conventional computer graphics cards are capable of generating images with 8-bit gray level resolution. However, most experiments in vision research require displays with more than 12 bits of luminance resolution. Several solutions are available. Bit++ ¹ and DataPixx ² use the Digital Visual Interface (DVI) output from graphics cards and high resolution (14 or 16-bit) digital-to-analog converters to drive analog display devices. The VideoSwitcher ³ described here combines analog video signals from the red and blue channels of graphics cards with different weights using a passive resister network ⁴ and an active circuit to deliver identical video signals to the three channels of color monitors. The method provides an inexpensive way to enable high-resolution monochromatic displays using conventional graphics cards and analog monitors. It can also provide trigger signals that can be used to mark stimulus onsets, making it easy to synchronize visual displays with physiological recordings or response time measurements.Although computer keyboards and mice are frequently used in measuring response times (RT), the accuracy of these measurements is quite low. The RTbox is a specialized hardware and software solution for accurate RT measurements. Connected to the host computer through a USB connection, the driver of the RTbox is compatible with all conventional operating systems. It uses a microprocessor and high-resolution clock to record the identities and timing of button events, which are buffered until the host computer retrieves them. The recorded button events are not affected by potential timing uncertainties or biases associated with data transmission and processing in the host computer. The asynchronous storage greatly simplifies the design of user programs. Several methods are available to synchronize the clocks of the RTbox and the host computer. The RTbox can also receive external triggers and be used to measure RT with respect to external events. Both VideoSwitcher and RTbox are available for users to purchase. The relevant information and many demonstration programs can be found at http://lobes.usc.edu/.     

Dynamic modeling of chemical reactions: the diels-alder cycloaddition

In order to visualize the stereochemical aspects of the Diels-Alder model cycloaddition of ethylene on butadiene, we developed a computer graphics animated model. The structural data base was deduced from MINDO/3 calculations, and the application program makes it possible to display in detail the different steps of the reaction mechanism. The scope of the application has been enlarged by a similar representation of the Diels-Alder cycloaddition of bis (methylene)—2,3 bicyclo [2.2.1]heptane to ethylene. Both of these examples suggest that molecular graphics is an ideal tool for visualizing and understanding the stereochemistry of complex chemical reactions.     

Computer-aided design in protein engineering

The amino acid sequence of a protein can be engineered genetically to yield a molecule with modified or novel properties of clinical or industrial importance, through knowledge of the relationships between sequence, three-dimensional structure and function. Interactive computer graphics can display and model the structural information revealed by protein cyrstallography. In the absence of a suitable crystal structure, computer methods must predict protein conformation from sequence. The most powerful approaches for structure prediction are based on sequence homology or a more general analogy with known crystal structures. Improvements in these methods will require access to data bases containing the basic motifs of protein architecture.     

LOPAL and SCAMP: techniques for the comparison and display of protein structures

This paper describes two computer programs designed to assist in the comparison of protein structures. LOPAL (LOoP ALignment) applies a dynamic programming algorithm to the comparison of regions of protein three-dimensional (3D) structure and gives a similarity score and suggested sequence alignment with that score. SCAMP (Structure Comparison and Alignment of Multiple Proteins) is an interactive graphics program for the Evans and Sutherland PS300 graphics terminal that allows the simultaneous display, manipulation and pairwise least-squares fitting of up to nine independent structures. Together, LOPAL and SCAMP provide an integrated system for characterizing structural similarities in proteins with the aim of improving the accuracy of predicted protein structures. An application of these programs to loop regions in the immunoglobulin constant domains is illustrated.     

Modeling cation/anion-water interactions in functional aluminosilicate structures

A need for the computer simulation of hydration/dehydration processes in functional aluminosilicate structures has been noted. Full and realistic simulations of these systems can be somewhat ambitious and require the aid of interactive computer graphics to identify key structural/chemical units, both in the devising of suitable water-ion simulation potentials and in the analysis of hydrogen-bonding schemes in the subsequent simulation studies. In this article, the former is demonstrated by the assembling of a range of essential water-ion potentials. These span the range of formal charges from +4e to −2e, and are evaluated in the context of three types of structure: a porous zeolite, calcium silicate cement, and layered clay. As an example of the latter, the computer graphics output from Monte Carlo computer simulation studies of hydration/dehydration in calcium-zeolite A is presented.     

A computer program for on-line measurement, storage, analysis and retrieval of urodynamic data

A computer program is presented which allows for direct connection of a minicomputer to a urodynamic set-up. The program stores measured pressure and flow data in a random access disc file with minimal intervention of the urodynamicist, and enables the direct application of a number of methods of analysis to the data. The program is modular, and other analysis methods are easily added. Results of analyses are stored in the same disc file, and both results and measured data can be quickly and easily retrieved. The program is written in FORTRAN; hardware-dependent functions (analog input, graphics display, and random access disc storage) are implemented in subroutines (partly assembler) which can easily be replaced.     

The kinemage: a tool for scientific communication.

A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared and specified by the author(s) of a journal article, in order to better communicate ideas that depend on three-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program, such as the one described here (called MAGE), which presently runs on Macintosh computers. A utility (called PREKIN) helps authors prepare the kinemages. Kinemages are being implemented under the auspices of the Innovative Technology Fund.     

A kinematic model of the flexor tendons of the hand

The multi-joint model is a kinematic simulation of the long flexor tendons of the fingers. The tendons modeled are the flexor pollicis longus, the flexor digitorum profundus, and the flexor digitorum superficialis. The simulated tendons are displayed on an Evans and Sutherland PS330 color graphics terminal attached to a display of articulated bones of the hand. As a user changes the position of the joints of the simulated hand, the simulation displays the new tendon path and the excursion of the tendon for the new position of the hand. The multi-joint model is one component of a comprehensive model for use in a hand biomechanics computer workstation.     

A microcomputer program for hydropathic analysis of proteins with I/O through word processing and graphics software

A BASIC program has been devised for the hydropathic analysisof protein sequences according to the method of Kyte and Doolittle(1982). The program uses sequence data from input files thatare created with a word processor and produces two types ofoutput file: one contains a bar graph of the hydropathic profilein a format that can be easily edited; the other is a tabulationof hydropathic indices along a protein's sequence that can beused as input by the program for the production of a bar graphor as input into other graphics and analysis software. An MS-DOSmicrocomputer, operating under IBM BASICA or GWBASIC and a dotmatrix printer with block graphics capabilities are the onlyhardware requirements for graphic display of hydropathy profiles.The program is capable of unattended analysis from a list ofup to 15 input files. ; accepted on March 10, 1986