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Results for “computational design”

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At least 343 records · Page 19Linked to original sources
PubMed2005

Highly active mutants of carbonyl reductase S1 with inverted coenzyme specificity and production of optically active alcohols.

A wild type NADPH-dependent carbonyl reductase from Candida magnoliae (reductase S1) has been found not to utilize NADH as a coenzyme. A mutation to exchange the coenzyme specificity in reductase S1 has been designed by computer-aided methods, including three-dimensional structure modeling and in silico screening of enzyme mutants. Site-directed mutagenesis has been used to introduce systematic substitutions of seven or eight amino acid residues onto the adenosine-binding pocket of the enzyme according to rational computational design. The resulting S1 mutants show NADH-dependency and have lost their ability to utilize NADPH as a coenzyme, but retain those catalytic activities. Kinetic parameter V(max) and K(m) values of those mutants for NADH are 1/3- to 1/10-fold those of the wild type enzyme for NADPH. As a model system for industrial production of optically active alcohols, the S1 mutants can be applied to an asymmetric reduction of ketones, cooperating with a coenzyme-regeneration system that uses an NAD-dependent formate dehydrogenase.

Alcohol Oxidoreductases↗
PubMed1993

Advances and current research in ceramic restorative materials.

Ceramics are currently the most widely used material for veneering crowns and bridges. Newer applications, such as bonded inlays, onlays, and veneers, are steadily gaining in popularity. A new generation of metal-free, all-ceramic systems for crowns became available during the 1980s. More recently, other all-ceramic systems with improved mechanical properties affording a variety of uses have been introduced. Also, a computer-assisted design-computer-assisted manufacture method of fabricating ceramic inlays has become a routine treatment entity with favorable 5-year clinical data. Research is leading to a better understanding of conventional ceramic systems as well as providing information on laboratory manipulation and clinical methodology for optimal results.

Crowns↗
PubMed1992

[A study of the computer aid design for tooth arrangement of full denture].

This paper is to use the power function Simpson's integration formula and some other methods to describe the geometric form of the dentition and edentulous arch in accordance with the theories and principles of tooth arrangement in textbook. The matching equations of artificial dentition and edentulous arch form and size are developed by using the multivariable regression method to analyze and summarize the clinical experiences of prosthodontists. Based on the above facts, a computer program that can be used to aid the dentist to arrange the artificial teeth for full denture is developed with Quick Basic Language and realized them in PC miniprocessors.

Computer-Aided Design↗
PubMed1999

Computational protein design.

A 'protein design cycle', involving cycling between theory and experiment, has led to recent advances in rational protein design. A reductionist approach, in which protein positions are classified by their local environments, has aided development of an appropriate energy expression. The computational principles and practicalities of the protein design cycle are discussed.

Algorithms↗
PubMed2004

JIDE: a new software for computer-aided design of hip prosthesis.

This work is aimed at developing an innovative simulation environment supporting and improving the design of standard joint implants (JPD integrated design environment (JIDE)). The conceptual workflow starts from the design of a new implant, by using conventional CAD programmes and completes with the generation of a report that summarises the goodness for a new implant against a database of human bone anatomies. For each dataset in the database, the JPD application calculates a set of quantitative indicators that will support the designer in the evaluation of its design on a statistical basis. The resulting system is thus directed to prostheses manufacturers and addresses a market segment that appears to have a steady growth in the future.

Computer Simulation↗
PubMed2003

Prudent modeling of core polar residues in computational protein design.

Hydrogen bond interactions were surveyed in a set of protein structures. Compared to surface positions, polar side-chains at core positions form a greater number of intra-molecular hydrogen bonds. Furthermore, the majority of polar side-chains at core positions form at least one hydrogen bond to main-chain atoms that are not involved in hydrogen bonds to other main-chain atoms. Based on this structural survey, hydrogen bond rules were generated for each polar amino acid for use in protein core design. In the context of protein core design, these prudent polar rules were used to eliminate from consideration polar amino acid rotamers that do not form a minimum number of hydrogen bonds. As an initial test, the core of Escherichia coli thioredoxin was selected as a design target. For this target, the prudent polar strategy resulted in a minor increase in computational complexity compared to a strategy that did not allow polar residues. Dead-end elimination was used to identify global minimum energy conformations for the prudent polar and no polar strategies. The prudent polar strategy identified a protein sequence that was thermodynamically stabilized by 2.5 kcal/mol relative to wild-type thioredoxin and 2.2 kcal/mol relative to a thioredoxin variant whose core was designed without polar residues.

Amino Acid Sequence↗
PubMed1996

Analysis of the catalytic mechanism of a fungal lipase using computer-aided design and structural mutants.

Both an active enzyme conformation and stabilization of tetrahedral transition states are essential for the catalysis of ester bond hydrolysis by lipases. X-ray structural data and results from site-directed mutagenesis experiments with proteases have been used as a basis for predictions of amino acid residues likely to have key functions in lipases. The gene encoding a lipase from Rhizopus oryzae was cloned and expressed in Escherichia coli. Site-directed mutagenesis of this gene was used to test the validity of computer-aided predictions of the functional roles of specific amino acids in this enzyme. Examination of the kinetic constants of the Rhizopus oryzae lipase variants allowed us to identify amino acid residues which are directly involved in the catalytic reaction or which stabilize the active geometry of the enzyme. The combination of these results with molecular mechanics simulations, based on a homology-derived structural model, provided new information about structure-function relationships. The interpretation of the data is consistent with results obtained with other hydrolases, such as proteases.

Amino Acid Sequence↗
PubMed1997

Effectiveness of computer-aided removable partial denture design.

PURPOSE: Computer programs have been developed for removable partial denture (RPD) design, but their educational impact has never been investigated. This study measured the effectiveness of computer-based RPD design simulations in a traditional RPD design course for second-year dental students. MATERIALS AND METHODS: Thirty-six students were randomly assigned to four groups, two simulation and two control groups, at the beginning of the RPD design module. A cross-over design compared the two strategies during laboratory exercises. First, the simulation group worked with the simulation, while the control group met in small-group seminars with faculty. Post-test 1 was given, and then students switched teaching methods and post-test 2 was given. Each post-test had two parts. Part 1 involved designing an RPD based on specific patient criteria. Part 2 involved choosing the more correct of the two designs. RESULTS: Results showed a significant difference (p = .0072) in two of four test groups. Although it was an initial evaluation, the computer simulation was shown to be equivalent to faculty-led small-group seminars. Students also responded positively to a questionnaire on their perceived effectiveness of the simulations. CONCLUSIONS: The results suggest that RPD design can be taught as effectively with computer-based simulations as with faculty-led seminars.

Computer-Aided Design↗
PubMed1992

Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida.

What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded beta-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Finger-clasp, a dimer of interdigitating beta-beta-alpha units, the simplest variant of the "handshake" structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather--a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.

Algorithms↗
PubMed2005

[The inlay computer aided design based on reverse engineering technology].

OBJECTIVE: This study was to explore a CAD method for constructing occlusal and proximal surfaces of inlays using reverse engineering (RE) software and to develop a CAD software for the inlay fabrication. METHODS: The dentition model of a volunteer with individual normal occlusion was scanned with a 3D mechanical scanner. The scanned objects were prepared teeth with G. V. Black class I, class II and class VI (MOD) cavities, neighbor teeth, intercuspal position (ICP) record, and functional bite record (or functional generate path, FGP). Inlays were constructed based on RE technology using the database of Chinese normal teeth. RESULTS: The technique guideline of inlay CAD was developed based on RE softwares. Inlays designed with CAD technique showed smooth and continuous contours. The occlusal and proximal contacts of inlay met physiologic demands. CONCLUSIONS: It is a feasible method to develop a CAD software for inlay fabrication based on RE software.

Adult↗
PubMed1995

Computer-aided design and fabrication of an electron bolus for treatment of the paraspinal muscles.

PURPOSE: Demonstrate the technology for the design, fabrication, and verification of an electron bolus used in the preoperative irradiation of a mesenchymal chondrosarcoma in the paraspinal muscle region (T8-T12), in which the target volume overlay a portion of the spinal cord, both lungs, and the right kidney. METHODS AND MATERIALS: An electron-bolus design algorithm implemented on a three dimensional (3D) radiotherapy treatment planning system designed the bolus to yield a dose distribution that met physician-specified clinical criteria. Electron doses were calculated using a 3D electron pencil-beam dose algorithm. A computer-driven milling machine fabricated the bolus from modeling wax, machining both the patient surface and the beam surface of the bolus. Verification of the bolus fabrication was achieved by repeating the patient's computed tomography (CT) scan with the fabricated bolus in place (directly on the posterior surface of the prone patient) and then recalculating the patient's dose distribution using the 3D radiotherapy treatment planning system. RESULTS: A treatment plan using a 17-MeV posterior electron field with a bolus delivered a superior dose distribution to the patient than did the same plan without a bolus. The bolus plan delivered a slightly increased dose to the target volume as a result of a slightly broader range of doses. There were significant reductions in dose to critical structures (cord, lungs, and kidney) in the bolus plan, as evidenced by dose-volume histograms (DVHs). The patient dose distribution, calculated using CT scan data with the fabricated bolus, showed no significant differences from the planned dose distribution. CONCLUSIONS: A bolus can provide considerable sparing of normal tissues when using a posterior electron beam to irradiate the paraspinal muscles. Bolus design and fabrication using the tools described in this paper are adequate for patient treatment. CT imaging of the patient with the bolus in place followed by calculation of the patient's dose distribution demonstrated a useful method for verification of the bolus design and fabrication process.

Adolescent↗
PubMed2006

The use of a Computer Aided Design (CAD) environment in 3D reconstruction of anatomic surfaces.

Paper presents an evaluation and comparison of two different types of software for generating a 3D model from medical imaging data: first, a dedicated 3D reconstruction Mimics interface, by Materialise and second, an engineering CAD (a Solid Works and AutoCAD) interface. Advantages and limitations of both software types are outlined and there some observations for 3D reconstruction of anatomic surfaces are presented.

Computer-Aided Design↗
PubMed2004

Computer aided designed neo-clavicle out of osteotomized free fibula: case report.

Total clavicle reconstruction is a challenging task. We performed a reconstruction of the ventral shoulder girdle by calculating a 3D DICOM representation of the left clavicle to create a right neo-clavicle. Two cuts in correct position and angle leads to a natural 3D shape of the new clavicle. The data were used with a thermo-jet procedure to form model slices of thermoplastic wax. Subsequently, the double titanium osteotomy template with correct cut-angulation was constructed. A 40-year old patient presented with symptoms of progressive pain and instability in the shoulder girdle resulting from complete right clavicle resection due to desmoid tumour 23 years earlier. During the operative procedure, dissection, guided double osteotomy, microvascular anastomoses and acromioclavicular-sternoclavicular fixation were performed. The computer-assisted planning resulted in the exact calculation of the two osteotomy cuts, hence, the 3D appearance of the neo-clavicle. Two years postoperatively, patient showed slightly improved elevation and complete recovery from pain. Our operative procedure demonstrates that the computer-assisted planning with construction of a wax model and an osteotomy template is a useful approach to plan the two precise cuts leading to a predictable shape of the clavicle.

Adult↗
PubMed2003

Medical devices; exemption from premarket notification; Class II devices; optical impression systems for computer assisted design and manufacturing. Final rule.

The Food and Drug Administration (FDA) is publishing an order granting a petition requesting exemption from the premarket notification requirements for data acquisition units for ceramic dental restoration systems. This rule exempts from premarket notification data acquisition units for ceramic dental restoration systems and establishes a guidance document as a special control for this device. FDA is publishing this order in accordance with the Food and Drug Administration Modernization Act of 1997 (FDAMA).

Computer-Aided Design↗
PubMed1991

A computer program designed for the analysis of data from rat caries studies.

The Keyes method for scoring dental caries in the rat animal model has been used as the basis for a computer-assisted scoring system on the Apple Macintosh personal computer that is described here. The program provides the ability to draw on diagrams of the rat molar dentition and to enter enamel lesion scores (L, E) and dentinal lesion scores (Ds, Dm, and Dx) for all aspects of the molars. The scores and drawings may be changed at any time. Total carious teeth and totals of L, E, Ds, Dm, and Dx are automatically calculated and presented upon user command. Error trapping for typographical errors is provided. In addition, the program provides automatic storage of the collected information, searching and sorting on any of the experimental parameters and on-disk help files that can be accessed from any place within the program. The capacity to obtain printed copy of any or all of the stored information is provided in the program. The program also enables the creation of external data files containing totals for carious teeth, in addition to L, E, Ds, Dm, and Dx totals for each animal of each group represented in the data base. These files are suitable for the transfer of data to commercially available programs for graphical and statistical analyses. The programming technique we describe could be extended to other model systems with standardized scoring for oral disease.

Animals↗
PubMed2005

Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase.

Design principles are delineated for non-nucleoside inhibitors for HIV-1 reverse transcriptase (NNRTIs). Simultaneous optimization of binding affinity for wild-type RT, tolerance for viral mutations, and physical properties is pursued. Automated lead generation with the growing program BOMB, Monte Carlo simulations with free-energy perturbation theory for lead optimization, and property analysis with QikProp are featured. An initial 30 microM lead has been optimized rapidly to the 10 nM level.

Computer-Aided Design↗