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PubMed1989

Electron transport in sulfate-reducing bacteria. Molecular modeling and NMR studies of the rubredoxin--tetraheme-cytochrome-c3 complex.

A hypothetical model of the complex formed between the iron-sulfur protein rubredoxin and the tetraheme cytochrome c3 from the sulfate-reducing bacteria Desulfovibrio vulgaris (Hildenborough) has been proposed utilizing computer graphic modeling, computational methods and NMR spectroscopy. The proposed complex appears feasible on the basis of complementary electrostatic interaction and steric factors and is consistent with the data from NMR experiments. In this model, the non-heme iron atom of rubredoxin is in close proximity to heme 1 of cytochrome c3. The complex is stabilized by charge-pair interactions and hydrogen bonds. This complex is compared to the flavodoxin-cytochrome c3 complex previously proposed [Stewart, D. E., LeGall, J., Moura, I., Moura, J. J. G., Peck, H. D. Jr, Xavier, A. V., Weiner, P. K. & Wampler, J. E. (1988) Biochemistry 27, 2444-2450] and new NMR data shows that both proteins interact with the same heme group of the cytochrome as postulated.

Binding Sites↗
PubMed1990

Computer applications in orthopaedics.

With the rapid developments in microprocessors, the widespread availability of computers has brought about broad applications in the field of orthopaedics. The present technology enables large quantities of data to be logically processed in a very short span of time. This has led to the development of information management database systems where relevant medical information may be retrieved very quickly and effectively. The analytical power of the computer has also been utilised in expert systems to assist in clinical-decision making process. Computer graphics have revolutionised the visualisation of physical features of internal and external body parts, providing new and improved modalities of diagnosis. In some centres, surgical planning and rehearsals are already being carried out at the computer terminal with the use of animation and computer graphics. Computer technology has also played an active role in the field of prosthetics and rehabilitation. Intelligent robotic systems and microprocessor with functional neuromuscular stimulation have been applied to benefit, and in some cases restore some motor functions to the physically disabled. With more collaboration between engineers, scientists and the medical community, several prototypes of computer-controlled prostheses and prosthesis designed and manufactured by Computer-Aided Design/Computer-Aided Manufacturing (CAD/CAM) technology are available today to assist the amputees in their daily living and ambulatory activities.

Computer Graphics↗
PubMed1992

Radioimmunoassay data handling and calculations with a graphics-statistics computer program.

This paper discusses the application of the data handling-graphics-statistics program Stata (Computing Resources Center, Santa Monica, CA) to radioimmunoassay. We have found that this program is more powerful and easier to use than a spreadsheet for analyzing various kinds of laboratory data generated from chromatography, radiolabeling experiments, enzyme-linked immunosorbent assays, and radioimmunoassays, to name several examples. Data from a radioimmunoassay procedure, originally analyzed using a spreadsheet, Lotus 1-2-3, have been processed with Stata. Simple programs (batch files) have been devised for computations and graphics. The original data and a comparison of results are presented.

Radioimmunoassay↗
PubMed1986

Development of electrocardiographic teaching materials using an MC68000-based, interactive graphics microcomputer.

Interactive computer-graphics methods of computer-aided design (CAD) have been applied to problems in physical science and industry for several years; however, at the present time CAD methods have not been widely used to solve similar problems in medical education. Electrocardiogram waveform fabrication for the production of teaching materials seemed to be a well-defined area for CAD application. The availability of inexpensive, 16/32 bit word, MC68000-based microcomputers (e.g. Apple, Macintosh) and interactive graphics software (e.g. MacPaint and MacDraw) seemed to provide the necessary tools to make this application. This paper describes the authors' initial experience (from June 1984 to March 1985) in developing and employing an interactive computer graphics routine to produce ECG teaching materials.

Cardiovascular Diseases↗
PubMed1978

Interactive computer surface graphics approach to study of the active site of bovine trypsin.

A descriptive medium for the presentation of protein structure has been developed and used to evaluate the structure of the active site of bovine trypsin (EC 3.4.21.4). This technique, involving advanced computer graphics technology, permits the facile display of a representation of the molecular surface of proteins of known structure and employs color to code the structural or chemical features of this surface. Benzamidine derivatives were inserted into the benzamidine-binding site of trypsin and the binary inhibitor-trypsin complex was evaluated by using the computer-generated structure. On the basis of qualitative assessments of the contribution of electrostatic and hydrophobic forces to the binding energy associated with complex formation, we made predictions concerning the effects of interaction of benzamidine substituents and amino acid side chains upon the binding energy associated with inhibitor-protein binding. The computer display of the molecular surfaces of the binary complex of substituted benzamidines and trypsin permitted unique insight into the identity and chemical properties of the atoms that participate at the interface of the molecular surfaces of the inhibitor and the protein. The computer-generated molecular surface display can potentially be combined with quantitative definition of the physical forces involved in the interaction of molecular surfaces. This technology should facilitate the study of the structure-activity relationship of substrates, inhibitors, and drugs that bind to proteins of known three-dimensional structure.

Animals↗
PubMed1992

[Comparison of fingerprints using a personal computer and graphic software sold on market].

We compared the fingerprint images using a personal computer and a graphic software sold on market. The fingerprints of thumb of left hand recorded by pressing and rolling on paper were input in computer using image scanner. These two fingerprint images were overlapped by moving and rotation on the computer screen, and were fitted well. This result showed that the fingerprints recorded by any way from one person were fitted. Latent and accused's fingerprints were also input in computer using image scanner. These images were analyzed by the same procedure. These two fingerprints were part by unfitting. It was decided these two fingerprints were not derived from one person. We also considered the possibility that the latent fingerprint was the reversed one. Then, the image was reversed of its color on the screen of computer (black to white and white to black) and compared by the same procedure. In this experiment, two fingerprint images were not fitted in a part. This showed that the reversed fingerprint was also able to be analyzed by this procedure. For the comparison of fingerprints, this report showed the ability of the personal computer and software which can be obtained easily from market. Following the improvement of the hardware and software used in this examination in near future, the computerized identification of fingerprints like this study will become more accurate and convenient.

Computer Graphics↗
PubMed1991

Two-dimensional computer color graphics of gastric mucosal blood distribution in normal subjects and ulcer patients.

The mucosal blood volume in 20 to 24 different regions of stomach was estimated by reflectance spectrophotometry during endoscopy, and an image showing mucosal blood distribution was made by two-dimensional computer color graphics with the aid of a personal computer. In 55 normal controls, the estimated mucosal blood volume (EMBV) was greater in the corpus mucosa than in the antral mucosa, and less in the lesser curvature than in the greater curvature. The volume in the anterior and posterior walls was almost the same. In 15 patients with active gastric ulcers in the angular region, the EMBV was decreased in all regions in the stomach. In 37 patients with healing ulcers, the EMBV increased, resuming the same levels as in normal controls. However, the EMBV around the ulcer increased remarkably at this stage. In 35 patients with ulcers in the scarring stage, the distribution of the EMBV was similar to that in the normal controls. These hemodynamic changes were shown clearly in a color display with the aid of a personal computer. This method could offer new possibilities in endoscopic research.

Adult↗
PubMed1991

Model for the structure of formaldehyde dehydrogenase based on alcohol dehydrogenase.

The three-dimensional structure of rat liver formaldehyde dehydrogenase (FALDH), previously known as class III alcohol dehydrogenase, was constructed using computer graphics and computer programs developed for model building. The construction is based on horse liver alcohol dehydrogenase (EE-ADH), whose structure has been elucidated by X-ray crystallography. The high sequence homology between the two enzymes makes knowledge-based modelling feasible in this case. The model shows a remarkable similarity to horse liver alcohol dehydrogenase especially in the NAD-binding domain. Certain mutations, and the one insertion in FALDH compared to EE-ADH in particular, have cause important changes in the substrate binding site, and thus aliphatic alcohols have been replaced by hemi-thioacetals as favourable substrates.

Alcohol Dehydrogenase↗
PubMed1987

Laserprinter applications in a medical graphics department.

Our experience with the Apple Macintosh and LaserWriter equipment has convinced us that lasergraphics holds much current and future promise in the creation of line graphics and typography for the biomedical community. Although we continue to use other computer graphics equipment to produce color slides and an occasional pen-plotter graphic, the most rapidly growing segment of our graphics workload is in material well-suited to production on the Macintosh/LaserWriter system. At present our goal is to integrate all of our computer graphics production (color slides, video paint graphics and monochrome print graphics) into a single Macintosh-based system within the next two years. The software and hardware currently available are capable of producing a wide range of science graphics very quickly and inexpensively. The cost-effectiveness, versatility and relatively low initial investment required to install this equipment make it an attractive alternative for cost-recovery departments just entering the field of computer graphics.

Computer Graphics↗
PubMed1986

Three-dimensional reconstructions of objects from serial sections using a microcomputer graphics system.

A computer graphics system for constructing 3-dimensional models of tissues from serial sections has been designed around a Motorola 68000 CPU. The system consists of a Dual Systems 16-bit microcomputer running the UNIX operating system. A Scion Corporation MicroAngelo color graphics system drives the color monitor. Three-dimensional imaging is enhanced by hidden line removal and area filling by color. A computer-drawn model of a cherry angioma is compared with a previously constructed physical model of the same angioma to illustrate how the system operates.

Computers↗
PubMed1986

Modeling complex molecular interactions involving proteins and DNA.

We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.

Base Sequence↗
PubMed1985

Computer-assisted analysis of ligament constraints in the knee.

A computer graphics technique was employed to investigate the ligament constraints in the knee joint. A computer-assisted tomography scan system was employed to obtain the geometry of the knee and the ligament insertion locations. A cadaver knee was mounted in a special rig that kept the femur and the tibia in a specified position. The scans of the knee at 5-mm distances were recorded. These scans were projected in the computer to generate a data base for the tibia, the femur, and the tibial and femoral insertion locations for the various ligaments. The computer graphics analysis provides realistic views of the bone structures. The views compare favorably with the original CT scans. Interestingly, the scans near the ligament insertion site were clearly observed to have a higher bone density. Higher density was also observed at the intercondylar notch below the patella. The analysis was used to simulate ACL and PCL insufficiencies. A Lachman test at 25 degrees of flexion is a sensitive test for ACL insufficiency, whereas the 90 degrees drawer test may not be a sensitive indicator of PCL insufficiency. This computer graphics technique may prove useful in the design and development of artificial ligaments as well as in planning surgical procedures.

Biomechanical Phenomena↗
PubMed1985

Prism representation: a 3D ray-tracing algorithm for radiotherapy applications.

Computing the intersection of a line with a volume, or 'ray tracing' as it is commonly known, is an integral component of three-dimensional radiotherapy dose calculation algorithms. Examples of ray tracing include the intersection of a ray from the radiation source with the patient, with heterogeneous volumes within the patient and with beam-modifying devices, such as a wedge or compensator. Ray tracing is also of primary importance in the field of three-dimensional computer graphics. Through the process of ray tracing, various display features, such as hidden surfaces, shadows, reflection and refraction, can be rendered simply and with startling realism. Advances have recently been made in three-dimensional ray-tracing methods in computer graphics. Due to the similarity of ray tracing in three-dimensional computer graphics and radiotherapy, these new techniques have an immediate application to the ray-tracing problems in three-dimensional radiotherapy dose calculations. The purpose of this paper is to present these advances and illustrate their use in radiation therapy.

Humans↗
PubMed1987

Comparison of computer modelling and X-ray results of the binding of a pyrazole derivative to liver alcohol dehydrogenase.

The binding to liver alcohol dehydrogenase of the inhibitor 2,4-(4-pyrazolyl)-butylisothiourea has been studied both by modelling experiments using computer graphics with interactive energy minimization and by X-ray crystallographic structure determination. For the modelling experiments, we used the program system TOM, which was developed in our laboratory as an extension of the program FRODO. Different strategies for using computer graphics with interactive energy minimization were tested. Two essentially different binding modes were found. One of these was favoured from energy minimizations using a potential energy function which was the sum of a Coulomb interaction term and two different van der Waals' interaction terms for non-bonded and torsional interactions. This binding mode was close to the crystallographic observed structure. The results show that flexibility of both ligand and receptor side-chains as well as main-chain conformations are important for docking to the active site of liver alcohol dehydrogenase.

Alcohol Dehydrogenase↗