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PubMed1992

Computer-aided gene design.

A computer program, which runs on MS-DOS personal computers, is described that assists in the design of synthetic genes coding for proteins. The goal of the program is the design of a gene which (i) contains as many unique restriction sites as possible and (ii) uses a specific codon usage. The gene designed according to the criteria above is (i) suitable for 'modular mutagenesis' experiments and (ii) optimized for expression. The program 'reverse-translates' protein sequences into degenerated DNA sequences, generates a map of potential restriction sites and locates sequence positions where unique restriction sites can be accommodated. The nucleic acid sequence is then 'refined' according to a specific codon usage to remove any degeneration. Unique restriction sites, if potentially present, can be 'forced' into the degenerated nucleic acid sequence by using 'priority codes' assigned to different restriction sequences.

Amino Acid Sequence↗
PubMed2002

Protein flexibility and computer-aided drug design.

Although computational techniques are increasingly being used in computer-aided drug design, the effects due to protein flexibility are still ignored in many applications. This review revisits rigorous statistical mechanical methods for predicting binding affinity, discusses some recent developments for improving their speed and reliability, and examines faster approximate models for facilitating virtual screening and lead optimization.

Computational Biology↗
PubMed2003

A data mining technique for discovering distinct patterns of hand signs: implications in user training and computer interface design.

Hand signs are considered as one of the important ways to enter information into computers for certain tasks. Computers receive sensor data of hand signs for recognition. When using hand signs as computer inputs, we need to (1) train computer users in the sign language so that their hand signs can be easily recognized by computers, and (2) design the computer interface to avoid the use of confusing signs for improving user input performance and user satisfaction. For user training and computer interface design, it is important to have a knowledge of which signs can be easily recognized by computers and which signs are not distinguishable by computers. This paper presents a data mining technique to discover distinct patterns of hand signs from sensor data. Based on these patterns, we derive a group of indistinguishable signs by computers. Such information can in turn assist in user training and computer interface design.

Algorithms↗
PubMed1988

Issues and themes in computer aided design for external prosthetics and orthotics.

Computer aided design systems are finding use in prosthetics and orthotics in the production of customized components to match to and support body segments. Such systems consist essentially at present of shape measurement, computer manipulation of shape, and manufacture of the support surface or its mould. General themes of design philosophy, relationship of shape and pressure for body segments, representation and presentation of shape information by computer, surface adjustments, measurements and manufacturing geometry are considered. Aspects of existing systems are presented to highlight issues which may be the subject of future developments.

Computer Graphics↗
PubMed2006

Computational protein design: a novel path to future protein drugs.

Computational protein design emerges in recent years as a field that could make a substantial impact on the design of protein drugs. It still consists mainly of redesigning parts of a protein sequence for increasing the stability of a given 3-dimensional conformation of a protein, but has already been extended from redesigning core residues to redesigning in all other protein regions, as well as to the design of backbone conformations. More recently, proteins with new binding functions and new enzymes, protein libraries, designs of full folds and of a new protein fold, have been some of the main highlights. The search and the scoring problems are however not fully solved, and many of the design processes should be examined on much larger scales in order to assess their usefulness. We examine some of the basic assumptions in computational protein design, in particular, the separation between sequence and scaffold designs. Among others, we suggest to include more protein residues in computations, to include relevant parts of the backbone, to use appropriate reference states, to produce the proteins and to validate the designs by structural examination of the protein products.

Computational Biology↗
PubMed2003

A general framework for brain-computer interface design.

The Brain-Computer Interface (BCI) research community has acknowledged that researchers are experiencing difficulties when they try to compare the BCI techniques described in the literature. In response to this situation, the community has stressed the need for objective methods to compare BCI technologies. Suggested improvements have included the development and use of benchmark applications and standard data sets. However, as a young, multidisciplinary research field, the BCI community lacks a common vocabulary. As a result, this deficiency leads to poor intergroup communication, which hinders the development of the desired methods of comparison. One of the principle reasons for the lack of common vocabulary is the absence of a common functional model of a BCI System. This paper proposes a new functional model for BCI System design. The model supports many features that facilitate the comparison of BCI technologies with other BCI and non-BCI user interface technologies. From this model, taxonomy for BCI System design is developed. Together the model and taxonomy are considered a general framework for BCI System design. The representational power of the proposed framework was evaluated by applying it to a set of existing BCI technologies. The framework could effectively describe all of the BCI System designs tested.

Algorithms↗
PubMed2002

Modulating calmodulin binding specificity through computational protein design.

We report the computational redesign of the protein-binding interface of calmodulin (CaM), a small, ubiquitous Ca(2+)-binding protein that is known to bind to and regulate a variety of functionally and structurally diverse proteins. The CaM binding interface was optimized to improve binding specificity towards one of its natural targets, smooth muscle myosin light chain kinase (smMLCK). The optimization was performed using optimization of rotamers by iterative techniques (ORBIT), a protein design program that utilizes a physically based force-field and the Dead-End Elimination theorem to compute sequences that are optimal for a given protein scaffold. Starting from the structure of the CaM-smMLCK complex, the program considered 10(22) amino acid residue sequences to obtain the lowest-energy CaM sequence. The resulting eightfold mutant, CaM_8, was constructed and tested for binding to a set of seven CaM target peptides. CaM_8 displayed high binding affinity to the smMLCK peptide (1.3nM), similar to that of the wild-type protein (1.8nM). The affinity of CaM_8 to six other target peptides was reduced, as intended, by 1.5-fold to 86-fold. Hence, CaM_8 exhibited increased binding specificity, preferring the smMLCK peptide to the other targets. Studies of this type may increase our understanding of the origins of binding specificity in protein-ligand complexes and may provide valuable information that can be used in the design of novel protein receptors and/or ligands.

Amino Acid Sequence↗
PubMed1982

Additional power computations for designing comparative Poisson trials.

Published power computations for designing comparative Poisson trials are extended to the case of unequal populations sizes. The goal is to determine the required duration of a study for testing the one-sided alternative that the incidence rate of a rare disease in one population exceeds that in another population, based on an exact test conditional on the total number of events observed. Tables are provided for two designs: observing until a predetermined number of events have been observed, or observing for a predetermined length of time. The results may also be used to determine sample sizes for comparative binomial trials with very small binomial parameters when the numbers of patients in the two groups are not necessarily equal.

Epidemiologic Methods↗
PubMed2003

Exact rotamer optimization for protein design.

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.

Algorithms↗
PubMed2006

Utilizing gamma band to improve mental task based brain-computer interface design.

A common method for designing brain-computer Interface (BCI) is to use electroencephalogram (EEG) signals extracted during mental tasks. In these BCI designs, features from EEG such as power and asymmetry ratios from delta, theta, alpha, and beta bands have been used in classifying different mental tasks. In this paper, the performance of the mental task based BCI design is improved by using spectral power and asymmetry ratios from gamma (24-37 Hz) band in addition to the lower frequency bands. In the experimental study, EEG signals extracted during five mental tasks from four subjects were used. Elman neural network (ENN) trained by the resilient backpropagation algorithm was used to classify the power and asymmetry ratios from EEG into different combinations of two mental tasks. The results indicated that ((1) the classification performance and training time of the BCI design were improved through the use of additional gamma band features; (2) classification performances were nearly invariant to the number of ENN hidden units or feature extraction method.

Algorithms↗
PubMed1998

Analysis of optimal range of socket orientations in total hip arthroplasty with use of computer-aided design simulation.

A three-dimensional computer-aided design model of a total hip replacement was used to study the effects of anteversion and abduction of the acetabular component and anteversion and varus-valgus angulation of the femoral component on the range of hip flexion and extension that could be obtained without component impingement. Impingement of the component was defined as impingement between the neck of the femoral component and the edge of the acetabular component. To achieve an angle of hip flexion greater than 90 degrees and an extension angle greater than 30 degrees without component impingement, the optimal angulations were found to be between 1 and 30 degrees of anteversion and 30 and 50 degrees of abduction of the acetabular component, as well as 10 degrees of anteversion of the femoral component. When the valgus angulation of the femoral component was reduced from 7 to 0 degrees, the allowable range of flexion without impingement increased under the same conditions of acetabular-component orientation and femoral-component anteversion. Significant inverse correlations were found between the anteversion angle of the acetabular component and both the lumbar lordosis angle and the sacrohorizontal angle.

Acetabulum↗
PubMed1995

GAP: a computer-assisted design tool for the development and analysis of evidence-based automated questionnaires.

This paper describes the design and use of a computer-assisted design tool for developing evidence-based automated questionnaires that may assist health practitioners to implement clinical practice guidelines. The Guideline Application Program (GAP) facilitates the design, development, testing, customization, and implementation of interactive patient-computer questionnaires, the analysis of patient-derived information, and the clinical application of practice guidelines that require knowledge of multiple patient-specific characteristics. GAP is being used to create a variety of software applications for HealthQuiz and Microsoft Windows-compatible computers. GAP-generated applications are presently used to support preventive care guideline implementation in primary care settings, preoperative screening in anesthesia clinics, student health screening in Universities, hormone replacement counseling for peri-menopausal women, and patient-reported data collection in various clinical research projects.

Algorithms↗
PubMed2004

Simulated annealing: an effective stochastic optimization approach to computational library design.

We describe here a stochastic optimization protocol for computational library design based on the principle of simulated annealing (SA). We also demonstrate via computer simulation studies that the SA-guided diversity sampling affords higher information content than random sampling in terms of cluster hit rates. Using a tripeptoid library, we show that the SA guided similarity focusing provides important information about reagent selection for combinatorial synthesis. Finally, we report a system that employs the SA protocol for the simultaneous optimization of multiple properties during library design. We propose that the SA technique is an effective optimization method for computational library design.

Combinatorial Chemistry Techniques↗
PubMed1992

A knowledge-based computer-aided design and manufacturing system for total hip replacement.

A knowledge-based computer-aided design and manufacturing system (CAD-CAM) has been developed for total hip replacement. Knowledge-based refers to the fact that the design process is a computer program that has been provided with preprogrammed design rules. Compared with conventional CAD-CAM systems, the knowledge-based system is automated, requires less designer intervention, and increases the accuracy of the design process. The capabilities of the system make it ideal for the design of standard and custom total hip replacement. A full-fill, press-fit custom total hip replacement has been designed using the knowledge-based system. The early clinical results of a series of 37 replacements in 31 patients is described in this paper.

Adult↗
PubMed2005

New frontiers in calvarial reconstruction: integrating computer-assisted design and tissue engineering in cranioplasty.

Repair of large and complex calvarial defects remains a particular challenge for reconstruction. The paucity of techniques and materials emphasizes the need for alternative bone formation strategies. Recent integrative approaches suggest that successful reconstruction requires interdisciplinary teams, with surgeons interacting with imaging experts, materials scientists, and engineers. In this review, the authors present an overview of current materials used in calvarial reconstruction. Subsequently, progress in computer-designed prostheses, tissue engineering, and osteoinduction strategies is discussed. Finally, the authors discuss their experience with the integration of computer-aided fabrication of customized implants and tissue engineering for calvarial reconstruction.

Animals↗
PubMed2005

Near-surface damage--a persistent problem in crowns obtained by computer-aided design and manufacturing.

Robust dental systems obtained by computer-aided design and manufacture (CAD/CAM) have been introduced and, in parallel, the strength of the ceramic materials used in fabricating dental crowns has improved. Yet all-ceramic crowns suffer from near-surface damage, limiting their clinical success, especially on posterior teeth. Factors directly associated with CAD/CAM fabrication that contribute to the degree of damage include material selection and machining parameters and strategies. However, a number of additional factors also either create new damage modes or exacerbate subcritical damage, potentially leading to catastrophic failure of the crown. Such factors include post-fabrication manipulations in the laboratory or by the clinician, fatigue associated with natural occlusal function, and stress fields created by compliance or distortion within the supporting tooth structure and/or adhesive material holding the crown to the tooth. Any damage reduces the strength of a crown, increasing the probability of catastrophic failure. The challenge is to understand and manage the combination of competing damage initiation sites and mechanisms, limitations imposed by the demand for aesthetics, and biologically related constraints.

Ceramics↗
PubMedDate not supplied

Use of computer-aided design in the preparation of technical manuscripts.

Decreased computing costs and constantly improving capability are transforming microcomputers into general rather than specialized productivity tools. This has made it possible to increase personal productivity in ways that were not previously cost-effective. We are using computer-aided design (CAD) to prepare technical illustrations for chemical and geochemical manuscripts. CAD offers several advantages over hand-drawn illustrations. Chemical structures are stored in a library of shapes and may be combined or modified to form other structures in subsequent drawings. An original drawing only has to be drawn once with a computer. The drawing may then be scaled to any size and placed in a draft of a manuscript. Revisions require a fraction of the time needed to revise a drawing by hand. All or part of the drawing may be plotted to provide a sequence of drawings without changing the original drawing.

Computer Graphics↗