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At least 1,225 records · Page 68Linked to original sources
PubMed1988

Microcomputer-based three-dimensional stereoscopic macromolecular graphics display.

Software which permits an IBM AT and two IBM Professional Graphics Displays to be used to display high-quality three-dimensional space-filling stereoscopic images of macromolecules is described. Stereo image pairs generated on two screens are visually fused using a simple mirror system to provide binocular depth perception. Images are colored to identify atomic type, residue type, charge or hydrophobicity according to user-specified codes and can be rotated and rescaled. Macromolecules containing over 16,000 atoms can be rapidly drawn using Brookhaven Protein Data Bank or user-supplied coordinates.

Computer Graphics↗
PubMed1988

A microcomputer program to evaluate the saturation of complex solutions with respect to biominerals.

The program described is written in BASIC and enables calculation of ionic activity products and degrees of saturation for solutions with respect to minerals of biological interest. The program takes into account ion-pair formation by association of anions and cations. The number of constituent species, whether or not involved in mineral formation or in ion-pair formation, appears to be unlimited. The computation fulfils the conditions of conservation of matter and electrical neutrality. Successful computation is achieved even for systems with highly unfavourable ratios between cations and anions with high affinities. The program is easily re-orientated towards any mineral/solution system.

Algorithms↗
PubMed1990

SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry.

A software package suitable for personal computers and designed to handle simulation and fitting problems related to the study of biomolecules under pre-steady and steady state conditions is presented, and its overall architecture as well as the implemented algorithms illustrated. The peculiar features of the package are: (i) integrated capability of simulating dynamic models and fitting to them experimental data; (ii) handling of stiff problems; (iii) free use of algebraic as well as differential equations; (iv) objective comparison of models of different complexity. The above features are discussed through a number of examples taken from the direct experience of the authors in enzyme kinetics and ligand binding.

Biochemical Phenomena↗
PubMed1991

An improved microcomputer program for finding gene- or gene family-specific oligonucleotides suitable as primers for polymerase chain reactions or as probes.

We present here an easy-to-use computer program which finds oligonucleotides suitable as primers in polymerase chain reactions (PCR) or as probes for hybridization. In contrast to other programs used for this purpose, the additional advantage of this one is the possibility of directly detecting gene- as well as gene family-specific oligonucleotides. For this purpose, up to 200 different DNA sequences, of maximally 65,000 nucleotides each, can be scanned in a single search to ensure either single or multiple gene binding of the PCR primers or probes. Specific oligonucleotides for genes carrying internal repetitions and for single genes belonging to a set of highly conserved genes can also be detected. Many parameters such as exclusion of simple sequences, which are known to be highly repeated throughout various genomes or regions of stable secondary structures in both primer-primer and primer-template, can be taken into consideration and avoided. Furthermore, the G + C content and the length of the oligonucleotides can be changed in a broad range by the user.

Animals↗
PubMed1992

DNABIND: an interactive microcomputer program searching for nucleotide sequences that may code for conserved DNA-binding protein motifs.

This paper presents a simple program for interactive searching for nucleotide sequences that may code for the helix-turn-helix, zinc finger or leucine zipper motifs in proteins. The helix-turn-helix motifs are predicted using the recently published method of Dodd and Egan, while zinc fingers and leucine zippers are searched for by our original methods. DNABIND is shown to detect all four known helix-turn-helix motifs in bacteriophage lambda genes and both zinc fingers of the adr1 gene of yeast.

Algorithms↗
PubMed1993

Microcomputer BASIC programs for rapid determination of lethal dosages of biocides using logit transformations.

The probit analysis model is generally used for the determination of lethal dosages in bioassay applications. However, the logit models, which use the logistic curve instead of the integrated normal curve, could also be effectively used for the determination of lethal dosages and regression coefficients. In this paper, two types of logit models, namely minimum logit chi square and maximum likelihood, have been described in detail for the estimation of the parameters. The results of these two models are also compared with those of the probit model.

Animals↗
PubMed1993

UNIREP: a microcomputer program to find unique and repetitive nucleotide sequences in genomes.

We present a program UNIREP, written in PowerBASIC for IBM-PCs, that identifies repetitive and unique nucleotide sequences in genomes or parts of genomes. A key feature of the algorithm is an oligonucleotide representation in a numerical code to make possible a comparison of all pairs of oligonucleotides (including overlaps) occurring in the analyzed sequence. This comparison assigns a score to each oligonucleotide, reflecting its similarity/dissimilarity to other oligonucleotides of the same length in the analyzed sequence. The score is plotted along the sequence so that peaks in the plot indicate repetitive regions and very low values reflect unique sequences. The scores are filtered to suppress or enhance the unique or repetitive sequences according to the user's wish. UNIREP is extended by auxiliary programs HIGHER and LOWER to list nucleotide sequences that have scores higher or lower than given limits. The potential of UNIREP is demonstrated using several long nucleotide sequences including the complete genomic sequence of EBV.

Algorithms↗
PubMed1989

Microcomputer-assisted liquid chromatographic separation system: application to toxic compounds identification in poisoned human fluids.

The computer-assisted liquid chromatographic system (MCASYST) is developed for automated identification and analysis. The system has six main functions: retention prediction system, liquid chromatographic data base system, automated identification system, optimization of separation conditions, data loading program from UV multichannel detector, and UV spectral data base system. The performance and potential of this MCASYST system is evaluated for toxic compounds identification in poisoned human fluids.

Body Fluids↗
PubMed1986

Estimation of sinoaortic baroreceptor heart rate reflex sensitivity and latency in man: a new microcomputer assisted method of analysis.

A new method for analysing baroreflex sensitivity has been developed. It obviates the mathematical bias inherent in earlier methods and in addition provides a direct measurement of reflex latency. Sensitivity results obtained using this method in 25 patients with a wide range of ages and resting blood pressures were similar to, but consistently lower than, those achieved with the Oxford method. Baroreflex latency results ranged from 650 to 2900 ms (mean(SD) 1084(427) ms) and were reproducible within individuals. Sensitivity results were inversely related to age and resting systolic blood pressure. Reflex latency was not related to these variables or to resting heart rate or reflex sensitivity. This method was able to identify inadequate starting data and greatly reduced the analysis time.

Adult↗