Computer-assisted rational drug design.
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Binding Sites↗
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Hardware implementation of fuzzy Petri net as a controller.
The paper presents a new approach to fuzzy Petri net (FPN) and its hardware implementation. The authors' motivation is as follows. Complex industrial processes can be often decomposed into many parallelly working subprocesses, which can, in turn, be modeled using Petri nets. If all the process variables (or events) are assumed to be two-valued signals, then it is possible to obtain a hardware or software control device, which works according to the algorithm described by conventional Petri net. However, the values of real signals are contained in some bounded interval and can be interpreted as events which are not only true or false, but rather true in some degree from the interval [0, 1]. Such a natural interpretation from multivalued logic (fuzzy logic) point of view, concerns sensor outputs, control signals, time expiration, etc. It leads to the idea of FPN as a controller, which one can rather simply obtain, and which would be able to process both analog, and binary signals. In the paper both graphical, and algebraic representations of the proposed FPN are given. The conditions under which transitions can be fired are described. The algebraic description of the net and a theorem which enables computation of new marking in the net, based on current marking, are formulated. Hardware implementation of the FPN, which uses fuzzy JK flip-flops and fuzzy gates, are proposed. An example illustrating usefulness of the proposed FPN for control algorithm description and its synthesis as a controller device for the concrete production process are presented.
Algorithms↗
Reconstruction of posttraumatic and congenital facial deformities with three-dimensional computer-assisted custom-designed implants.
The principles, method, and benefits of combining three-dimensional computed tomography (CT) and computer-aided design/computer-aided manufacture (CAD/CAM) technology for development of custom-designed prostheses are applied in the repair of posttraumatic and congenital facial contour deficiencies. Each prosthesis is generated to fit the bone defect exactly, with external contours adjusted to compensate for overlying soft-tissue disparities. Three representative case reports from a series of 17 demonstrate the applications and advantages of using this technique. Some patients had residual defects after primary repair of posttraumatic deformities. Others had defects after orthognathic relapses for congenital deformities. Without a relatively minor surgery and a high degree of predictability, many of these patients would not have pursued further treatment. All but one of the surgeries were performed on an outpatient basis, providing an accurate, simple, and cost-effective method of contour restoration with limited morbidity and reduced operative time.
Adult↗
The Bergmann Foot Scanner for automated orthotic fabrication.
The word automation sometimes can be misleading. I believe that some feel that automation of orthotic manufacturing results in a system in which orthotics are mass produced. Still others believe that the main reason for automation is to make orthotics quicker and cheaper and not individualized. As far as the author's laboratory is concerned, nothing could be further from the truth. We think of automation as the use of computer technology to make orthotics that are more accurate and more specialized as to the doctor's specific requirements. This is a method that takes the expertise of the podiatrist and the laboratory technician and gives them a tool that can be used to achieve the perfection in orthotic fabrication they are trying to attain. In testing out new types of cast correction designs, computer-designed images will give the repeatability needed in scientific research not found with manually applied corrections. The optical scanner has given us more than just a means of sending a cast to the laboratory quickly. It has turned out to be a method to help explain biomechanics of the patient's foot in a clear and concise way. We also have watched it develop into a research tool that podiatry schools and others can use to verify and further biomechanical principles.
Computer-Aided Design↗
Protein design is NP-hard.
Biologists working in the area of computational protein design have never doubted the seriousness of the algorithmic challenges that face them in attempting in silico sequence selection. It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard. The purpose of this paper is to explain the context of this observation, to provide a simple illustrative proof and to discuss the implications for future progress on algorithms for computational protein design.
Algorithms↗
MRI data compression using a 3-D discrete wavelet transform.
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Algorithms↗
Some computational aspects of theoretical anti-HIV drug design.
The three computational methods, the free energy perturbation (FEP), free energy derivative (FED) and continuum solvent molecular dynamics post analysis methods are presented. Application of the FEP method to improve binding properties of the aspartic protease JG-365 inhibitor has been demonstrated.
Anti-HIV Agents↗
Use of computer aided drafting for analysis and control of posture in manual work.
Computer aided design (CAD) in conjunction with digitised anthropometric manikins can be used for analysis and control of stressful work postures, one of the most frequently cited occupational risk factors of upper extremity cumulative trauma disorders. This paper describes the use of macros for manipulating manikins and workstation components and for designing the workplace. AutoCAD, a popular computer aided design software package, was used to demonstrate the feasibility of these concepts. Specifically, macros are used for drawing work equipment using parametric designs, manipulating manikins and analysing jobs. In comparing the macros to the use of primitive CAD commands, the macros not only decrease the amount of time needed to create workstation components, but they also make the task easier for the user and decrease the risk of errors. Despite the limitation of anthropometric data and manikins, CAD is an effective method for identifying postural stresses and redesigning the workstation to control the identified stresses.
Journal Article↗
The evolution of custom microarray manufacture.
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Computer-Aided Design↗
From Zurich to Sydney and back.
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Computer-Aided Design↗
Computer simulation in the design of local exhaust hoods for shielded metal arc welding.
Computer simulations were used to examine competing exhaust hood configurations for shielded metal arc welding. The welder's breathing zone concentration appears to be an inverse linear function of the computer-predicted hood capture efficiency. Hood aspect ratio, hood flow, and the welder's position relative to the hood all have a significant effect on the breathing zone concentration. The height of the hood above the welding surface showed no significant effect in reducing breathing zone concentration. Further examination of breathing zone concentration as a function of capture efficiency is needed before reliable design methods can be developed using this parameter.
Air Movements↗
A computationally efficient approach for the design of population pharmacokinetic studies.
A computationally efficient procedure was devised for designing experiments in which population pharmacokinetic parameters are estimated. The method, referred to as the large-sample approach, evaluates the variances of parameter estimates for a population pharmacostatistical model. The procedure utilizes the NONMEM program and requires a single simulation that assumes many, say 1000, subjects. The approach reduced CPU time by about a factor of 50 when compared with the evaluation of the same variances by the direct simulation of experiments. The large-sample and simulation approaches yielded generally similar values for the variances of parameter estimates. The variances calculated by the large-sample approach were, in the case of a simple model, close to the expected variances. The proposed method identified correctly the imprecise parameter estimates but somewhat underestimated their variances.
Computer Simulation↗
A CAD CAM method for custom below-knee sockets.
The purpose of this investigation was to develop a numerical method for fabricating prosthetic sockets for below-knee amputees. An optical/laser digitiser scans an amputee's stump and collects three dimensional numerical data describing the surface of the limb and describing specific modification site locations. The numerical data from the laser camera representing the stump and modification sites are altered by the prosthetist using a custom computer aided design software system running on a personal computer. Using the altered numerical data a programme is created for a high resolution numerically controlled milling machine and a mould is made. The prosthetist then fabricates a socket. While the system has been tested with below-knee amputees it has been designed for application in most areas of prosthetics and orthotics. Utilising this method 15 patients were fitted. All patients subjectively stated that their "computer designed" socket fitted better than their conventionally made socket. As the research progressed and experience was gained with the system patients were normally fitted with the first socket iteration. The system overcomes five limitations existing with some of the other numerical systems: 1) accurate high resolution surface topography, 2) specific identification of subject modification sites, 3) flexible, user friendly software, 4) high resolution numerically controlled milling, and 5) integrated expansion to other prosthetic and orthotic areas.
Artificial Limbs↗
[An introduction to the computer-aided structure-based drug design--applications of bioinformatics to drug discovery].
Computer-aided drug design methods are effective tools for drug discoveries. It is only small number of compounds that are required to be synthesized in practice, if the computer-aided drug design methods are used to predict the activities of the compounds. The methods are based on the interaction theory between drugs and their target proteins. Steric, electrostatic and hydrophobic complementarities are important in the interaction between the drug and the target protein. When three-dimensional structures of target proteins are known, the method is called as a structure-based drug design, while in case that the structures are unknown, a ligand-based drug design approach is employed for the computer-aided rational drug design. In the computer-aided structure-based drug design, it is important to build up the three-dimensional structure of drug-protein complex and to calculate a binding affinity of the drug to the protein. A molecular dynamics/free energy calculation is one of the most powerful tools to predict the binding affinity of a ligand molecule, when the three-dimensional structure of the drug-protein complex is available. The molecular dynamics/free energy calculation has been able to evaluate the binding affinities of a lot of ligand molecules to the target proteins successfully.
Computational Biology↗
Reagent-based and product-based computational approaches in library design.
The design of combinatorial libraries involves the consideration of all synthesizable compounds (the virtual library), followed by the selection of a suitably sized subset for actual synthesis and experimentation. Several approaches to this task can be envisaged, involving either reagent-based or product-based considerations. Reagent-based design considers the properties of the building blocks rather than those of the final products. Although popular with chemists, this approach overlooks the extent of chemical transformations involved in generating products. In effect, several important properties cannot be derived from building blocks alone and require access to product structures. Several studies have demonstrated the superiority of product-based designs in yielding diverse and representative subsets. Although more computationally intensive, the latter approach provides a basis for more sophisticated designs where reagent-based and product based considerations can be combined for a best-of-breed approach.
Computational Biology↗
Trends in indirect dentistry: 8. CAD/CAM technology.
UNLABELLED: Computer-aided design (CAD) and computer-aided manufacturing (CAM) of indirect restorations became available to dentistry over 15 years ago, providing replication and digitization of the complex topography of tooth structure. There are now many applications, providing better mechanical properties, improved marginal integrity and enhanced aesthetics, compared with traditional indirect techniques. Whether a restoration is fabricated by traditional or modern computerized systems, three functional stages are required; data acquisition, design and manufacture. It is the purpose of this paper to describe the applications of CAD and CAM in contemporary indirect dentistry. CLINICAL RELEVANCE: Reliable CAD/CAM techniques, some of which may reduce the number of patient visits, are now available for the production of a variety of ceramic restorations.
Ceramics↗
Computer interface and software analysis for multi-channel, on-line temperature recording to any micro-computer.
A simple, inexpensive computer interface designed for in vitro or in vivo researchers with limited electronic experience allows direct on-line multi-channel temperature recording from thermistor probes to any micro-computer. The designed system saves time and increases the accuracy of collected data that are ready for storage in files compatible with graphic and statistical software. In vitro testing of the designed interface, over a range of 25-45 degrees C, showed a 0.999 intraclass correlation to reference water bath temperatures. In vivo testing using anesthetized rats involved simultaneous measurements of: (1) a thermogenic tissue, interscapular brown adipose temperature (IBAT), (2) core (colonic) temperature, and (3) surface (tail) temperature, a heat loss tissue. The temperatures measured by the designed computer-interface demonstrate excellent stability, sensitivity and accuracy when compared to respective temperatures measured by a YSI telethermometer.
Animals↗
Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions.
Computer graphics modeling of the thyroxine-prealbumin complex provides a detailed picture of the interactions between thyroxine and prealbumin. A wide variety of thyroid hormone analogue-prealbumin complexes were modeled by calculating the molecular surfaces of the analogues and the prealbumin hormone-binding site. Analogues with high binding affinity were observed to fill more of the hormone-binding site than low-affinity analogues. These surface models described many aspects of the hormone-protein interaction which were not obvious using simple wire models and led us to develop a model which accounts for thyroid hormone-prealbumin structure-activity relationships and ultimately to predict and measure the relative binding affinities of four previously untested thyroid hormone analogues to prealbumin.
Chemical Phenomena↗