Tek FRODO: A new version of FRODO for Tektronix graphics stations

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. The work was divided into two parts: first, the universal molecular modeling graphic package (Tek_MMGP) was written to enable basic modeling operations for Tektronix stations. Second, all routines of FRODO involving computer graphics were modified to fit the new hardware environment, and linked with Tek_MMGP. The resulting package, Tek_FRODO, has been used successfully for crystallographic refinement in several projects. The program, written in FORTRAN, is ready to be ported to any of Tektronix 3D graphics stations; it is available from the authors on request.     

Consensus sequence Zen

Consensus sequences are widely used in molecular biology but they have many flaws. As a result, binding sites of proteins and other molecules are missed during studies of genetic sequences and important biological effects cannot be seen. Information theory provides a mathematically robust way to avoid consensus sequences. Instead of using consensus sequences, sequence conservation can be quantitatively presented in bits of information by using sequence logo graphics to represent the average of a set of sites, and sequence walker graphics to represent individual sites.     

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.     

Molecular graphics and the classical adiabatic and nonadiabatic dynamics of small polyatomic reactions

A molecular graphics system for displaying the classical trajectories of small polyatomic molecule dynamics has been developed. The system can be used in adiabatic and nonadiabatic dynamic studies. Applications to the photodissociation of water at 10e V illustrate the usefulness of computer graphics in molecular reaction dynamics.     

Single-scan stereotactic tumor biopsy and brachytherapy

Stereotactic tumor biopsy and brachytherapy catheter implantation can be accomplished with targets derived from computed axial tomography and magnetic resonance scans. Computer manipulation of image data allows both diagnostic and therapeutic procedures to be carried out from a single set of scan slices. This eliminates the need for repeat scanning as part of the surgical procedure. Microcomputer technology is sufficiently advanced to handle the images and graphics necessary for stereotactic neurosurgery. A system based on the IBM PC/AT designed for this purpose uses readily available graphics software and custom-designed imaging programs. Direct loading of computed axial or magnetic resonance scan images from magnetic tape can be accomplished. Determination of points, contours and volumes in three-dimensional space allows intraoperative alignment of image data and patient landmarks within the stereotactic head frame using pattern recognition overlays. Three-axis scaling for magnification correction along with rotational and linear data transformations provide the basis for single-scan stereotaxis. Interactive computer graphics integrate image, patient and frame coordinates for target determination. This method eliminates the need to design and fabricate nonmagnetic or radiolucent scanner-compatible devices.     

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.     

R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping

Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl’s static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data.     

The Understanding and Interpretation of Innovative Technology-Enabled Multidimensional Physical Activity Feedback in Patients at Risk of Future Chronic Disease

BackgroundInnovative physical activity monitoring technology can be used to depict rich visual feedback that encompasses the various aspects of physical activity known to be important for health. However, it is unknown whether patients who are at risk of chronic disease would understand such sophisticated personalised feedback or whether they would find it useful and motivating. The purpose of the present study was to determine whether technology-enabled multidimensional physical activity graphics and visualisations are comprehensible and usable for patients at risk of chronic disease.MethodWe developed several iterations of graphics depicting minute-by-minute activity patterns and integrated physical activity health targets. Subsequently, patients at moderate/high risk of chronic disease (n=29) and healthcare practitioners (n=15) from South West England underwent full 7-days activity monitoring followed by individual semi-structured interviews in which they were asked to comment on their own personalised visual feedback Framework analysis was used to gauge their interpretation and of personalised feedback, graphics and visualisations.ResultsWe identified two main components focussing on (a) the interpretation of feedback designs and data and (b) the impact of personalised visual physical activity feedback on facilitation of health behaviour change. Participants demonstrated a clear ability to understand the sophisticated personal information plus an enhanced physical activity knowledge. They reported that receiving multidimensional feedback was motivating and could be usefully applied to facilitate their efforts in becoming more physically active.ConclusionMultidimensional physical activity feedback can be made comprehensible, informative and motivational by using appropriate graphics and visualisations. There is an opportunity to exploit the full potential created by technological innovation and provide sophisticated personalised physical activity feedback as an adjunct to support behaviour change.     

Databases in molecular graphics

A survey of the computer graphics literature shows the importance of a link between a graphics facility and a database. This issue of Journal of Molecular Graphics includes three papers that cover uses of databases in chemical information retrieval and holding 3D molecular data. This editorial gives an introduction to this set of papers.     

Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction.

A program is described which calculates the thermal stability and the denaturation behaviour of double-stranded DNAs and RNAs up to a length of 1000 base pairs. The algorithm is based on recursive generation of conditional and a priori probabilities for base stacking. Output of the program may be compared directly to experimental results; thus the program may be used to optimize the nucleic acid fragments, the primers and the experimental conditions prior to experiments like polymerase chain reactions, temperature-gradient gel electrophoresis, denaturing-gradient gel electrophoresis and hybridizations. The program is available in three versions; the first version runs interactively on VAXstations producing graphics output directly, the second is implemented as part of the HUSAR package at GENIUSnet, the third runs on any computer producing text output which serves as input to available graphics programs.     

A computer graphics program system for protein structure representation

We have developed a computer graphics program system for the schematic representation of several protein secondary structure analysis algorithms. The programs calculate the probability of occurrence of alpha-helix, beta-sheet and beta-turns by the method of Chou and Fasman and assign unique predicted structure to each residue using a novel conflict resolution algorithm based on maximum likelihood. A detailed structure map containing secondary structure, hydrophobicity, sequence identity, sequence numbering and the location of putative N-linked glycosylation sites is then produced. In addition, helical wheel diagrams and hydrophobic moment calculations can be performed to further analyze the properties of selected regions of the sequence. As they require only structure specification as input, the graphics programs can easily be adapted for use with other secondary structure prediction schemes. The use of these programs to analyze protein structure-function relationships is described and evaluated.     

The cysteine protease of Trypanosoma cruzi as a model for antiparasite drug design

By combining new technology in molecular biology, X-ray crystallography, computer graphics and biochemistry, structure-based drug design provides a parallel and cost-effective strategy for identification of new antiparasite chemotherapy. James McKerrow, Mary McGrath and Juan Engel here discuss an example of the amplication of this strategy is its use in targeting the major cysteine protease in Trypanosoma cruzi. Tools from molecular biology helped overcome the obstacle of limited parasite material to allow production of reagent quantities of enzyme for inhibitor screening. Computer graphics analysis and X-ray crystallography are allowing rapid identification of new inhibitors based on either leads already identified or compounds selected by computer graphics screening of chemical databases.     

MOLECULAR DESIGNER: an interactive program for the display of protein structure on the IBM-PC

A BASIC interactive graphics program has been developed forthe IBM-PC which utilizes the graphics capabilities of thatcomputer to display and manipulate protein structure from coordinates.Structures may be generated from typed files, or from BrookhavenNational Laboratories' Protein Data Bank data tapes. Once displayed,images may be rotated, translated and expanded to any desiredsize. Figures may be viewed as ball-and-stick or space-fillingmodels. Calculated multiple-point perspective may also be addedto the display. Docking manipulations are possible since morethan a single figure may be displayed and manipulated simultaneously.Further, stereo images and red/blue three-dimensional imagesmay be generated using the accompanying DESIPLOT program andan HP-7475A plotter. A version of the program is also currentlyavailable for the Apple Macintosh. Full implementation on theMacintosh requires 512 K and at least one disk drive. Otherwisethis version is essentially identical to the IBM-PC versiondescribed herein. Received on July 12, 1985; accepted on August 1, 1985     

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.     

A colour editor for use in molecular raster graphics

An editor system is presented for a flexible definition of colour maps for use in raster graphics systems with frame buffers. This system - MONICOL - allows an easy display of 3D objects, particularly in molecular graphics. Some applications with respect to the representation of shaded objects and energy surfaces are given, as well as to a software solution of multiple layer buffering.     

A general approach to surface modelling applied to molecular graphics

A program is described that produces realistic representations of surfaces on a raster graphics terminal. The program uses a spatial subdivision algorithm similar to that of Woodwork and Quinlan. Simple geometric primitives, such as spheres, cones, cylinders and cuboids, are combined to build more complex pictures. This paper describes the program and how it is applied to molecular graphics. Examples of several applications are given.     

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.     

A Software Architecture for Multi-Cellular System Simulations on Graphics Processing Units

The first aim of simulation in virtual environment is to help biologists to have a better understanding of the simulated system. The cost of such simulation is significantly reduced compared to that of in vivo simulation. However, the inherent complexity of biological system makes it hard to simulate these systems on non-parallel architectures: models might be made of sub-models and take several scales into account; the number of simulated entities may be quite large. Today, graphics cards are used for general purpose computing which has been made easier thanks to frameworks like CUDA or OpenCL. Parallelization of models may however not be easy: parallel computer programing skills are often required; several hardware architectures may be used to execute models. In this paper, we present the software architecture we built in order to implement various models able to simulate multi-cellular system. This architecture is modular and it implements data structures adapted for graphics processing units architectures. It allows efficient simulation of biological mechanisms.     

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     

Comparison of protein structural profiles by interactive computer graphics

This paper describes a novel computer graphics tool for predicting protein structures. The method is based on structural profiles; which are plots of hydrophobicity, parameters used for secondary structure prediction, or other residue-specific traits against sequence number. Similar structural profiles can indicate similar tertiary structures, in the absence of sequence homology. The profiles of reference proteins, with known structure, can be used for prediction. In the method presented here, structural profiles are compared by interactive computer graphics, using the program Multiplot. As a test, a structural profile comparison of several proteins known to have similar 3D structures is presented. Comparison of structural profiles detects similar folding of the two domains of rhodanese, which was not easily detected by sequence homology.