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Results for “Computational methods”

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At least 235 records · Page 13Linked to original sources
PubMed2002

Discovery of regulatory elements by a computational method for phylogenetic footprinting.

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.

Algorithms↗
PubMed1991

The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme.

We review our research on triose-phosphate isomerase and bacteriophage T4 lysozyme. In our studies over the last ten years we have used electrostatic potentials, computer graphics, quantum mechanics, molecular mechanics, molecular dynamics and free energy calculations to try to understand why triose-phosphate isomerase is such an efficient enzyme and why its efficiency is dramatically decreased by several site-specific mutations. For T4 lysozyme we have used free energy methods to analyse and try to understand why Thr-157----Val and Thr-157----Ala mutations decrease protein stability by about 1-2 kcal/mol.

Amino Acid Sequence↗
PubMed2002

A fast and easy computational method to calculate the (13)C NMR chemical shift of organic species adsorbed on the zeolite surface.

Calculations of the 13C NMR chemical shifts for the methoxy and ethoxy groups adsorbed on Y and ZSM-5 zeolites were computed at GIAO/B3LYP/6-31+G*//MM+ level of theory, using a cluster representing a real part of the zeolites. The Y zeolite was represented by a cluster with 168 atoms, while ZSM-5 was represented by a cluster with 144 atoms. The calculated chemical shifts agreed well with reported experimental values, showing that the difference in chemical shifts is associated with differences in the geometry of the alkoxides on the two zeolites.

Journal Article↗
PubMed2000

A rapid computational method for lead evolution: description and application to alpha(1)-adrenergic antagonists.

The high failure rate of drugs in the development phase requires a strategy to reduce risks by generating lead candidates from different chemical classes. We describe a new three-dimensional computational approach for lead evolution, based on multiple pharmacophore hypotheses. Using full conformational models for both active and inactive compounds, a large number of pharmacophore hypotheses are analyzed to select the set or "ensemble" of hypotheses that, when combined, is most able to discriminate between active and inactive molecules. The ensemble hypothesis is then used to search virtual chemical libraries to identify compounds for synthesis. This method is very rapid, allowing very large virtual libraries on the order of a million compounds to be filtered efficiently. In applying this method to alpha(1)-adrenergic receptor ligands, we have demonstrated lead evolution from heterocyclic alpha(1)-adrenergic receptor ligands to highly dissimilar active N-substituted glycine compounds. Our results also show that the active N-substituted glycines are part of our smaller filtered library and thus could have been identified by synthesizing only a portion of the N-substituted glycine library.

Adrenergic alpha-Antagonists↗
PubMed1996

Computational methods in radionuclide dosimetry.

The various approaches in radionuclide dosimetry depend on the size and spatial relation of the sources and targets considered in conjunction with the emission range of the radionuclide used. We present some of the frequently reported computational techniques on the basis of the source/target size. For whole organs, or for sources of targets bigger than some centimetres, the acknowledged standard was introduced 30 years ago by the MIRD committee and is still being updated. That approach, based on the absorbed fraction concept, is mainly used for radioprotection purposes but has been updated to take into account the dosimetric challenge raised by therapeutic use of vectored radiopharmaceuticals. At this level, the most important computational effort is in the field of photon dosimetry. On the millimetre scale, photons can often be disregarded, and beta or electron dosimetry is generally reported. Heterogeneities at this level are mainly above the cell level, involving groups of cell or a part of an organ. The dose distribution pattern is often calculated by generalizing a point source dose distribution, but direct calculation by Monte Carlo techniques is also frequently reported because it allows media of inhomogeneous density to be considered. At the cell level, alpha and electron (low-range beta or Auger) are the predominant emissions examined. Heterogeneities in the dose distribution are taken into account, mainly to determine the mean dose at the nucleus. At the DNA level, Auger electrons or alpha-particles are considered from a microdosimetric point of view. These studies are often connected with radiobiological experiments on radionuclide toxicity.

Beta Particles↗
PubMed2001

Computational methods for protein function analysis.

Two recent advances have had the greatest impact on protein function analysis so far: the complete sequences of genomes and mRNA expression level profiles. The former has spurred the development of novel techniques to study protein function: phylogenetic profiles and gene clusters. The latter has introduced a method, not based on sequence homology, that enables one to group together functionally related genes.

Animals↗
PubMed1983

Testing a theory of brain function by computer methods. II. Timing short-range mental scanning.

In keeping with a plan for overall testing of the timing and sequencing of brain processes, testing techniques are introduced for timing short-range mental scanning without eye movement. The tests, using a personal computer, reveal the tendency to scan from left to right, even when there is insufficient time for eye movement, in persons whose first language is one which is read from left to right. The tests depend on the use of blocking stimuli which operate on central processes rather than peripheral processes, and suggest that it is possible to measure the timing and sequencing of central brain processing thereby.

Adult↗
PubMed1991

A computer method for visual presentation and programmed evaluation of labor.

Manual graphing of the progress of labor is considered useful but is not often done. The early detection of some deviations requires special graphics aids. Our objective was to develop an easy-to-use computer program for the integrated visual presentation of information characterizing the progress of labor. Through the use of inexpensive personal computers equipped with graphics monitors, the program provides a combined graphics display of timed progressive cervical dilatation, fetal station, and stimulation of uterine activity (oxytocin infusion). For the early detection of abnormalities, phase-specific normal ranges (reference areas) are displayed. In addition, protraction/arrest as well as precipitate labor disorders are highlighted and computer messages are displayed. The program was evaluated through the assessment of 405 labors entered into a local area network of computers. On average, the program identified 1.5 abnormalities per recorded labor (2.0 for labors resulting in vaginal delivery). The graphic presentation of the labor curve, produced within 3 seconds, displayed 27% more information than the tabular format on the same screen area and provided a single-screen display of the labor curve even for patients with excessive data. The computer-generated display of labor curves facilitates visual presentation and interpretation of labor progress and can also help to translate quality assurance criteria into clinical practice.

Computer Graphics↗
PubMed2000

A computational method for NMR-constrained protein threading.

Protein threading provides an effective method for fold recognition and backbone structure prediction. But its application is currently limited due to its level of prediction accuracy and scope of applicability. One way to significantly improve its usefulness is through the incorporation of underconstrained (or partial) NMR data. It is well known that the NMR method for protein structure determination applies only to small proteins and that its effectiveness decreases rapidly as the protein mass increases beyond about 30 kD. We present, in this paper, a computational framework for applying underconstrained NMR data (that alone are insufficient for structure determination) as constraints in protein threading and also in all-atom model construction. In this study, we consider both secondary structure assignments from chemical shifts and NOE distance restraints. Our results have shown that both secondary structure assignments and a small number of long-range NOEs can significantly improve the threading quality in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from homologs to analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a great amount of structural information, equivalent to that provided by many NMR data; and hence can help reduce the number of NMR data typically required for an accurate structure determination. This new technique can potentially accelerate current NMR structure determination processes and possibly expand NMR's capability to larger proteins.

Algorithms↗
PubMed1992

Computer methods for locating kinetoplastid cryptogenes.

RNA editing in the mitochondria of kinetoplastid protoza involves the insertion and/or deletion of precise numbers of uridine residues at precise locations in the numbers of uridine residues at precise locations in the transcribed RNA of certain genes. These genes are known as cryptogenes. In this paper we study computational algorithms to search for unknown cryptogenes and for the associated templates for insertion of uridines, gRNA sequences. The pairwise similarity search algorithm of Smith and Waterman (1) is modified to study this problem. The algorithm searches for unknown gRNAs given the cryptogene sequence. The method is tested on 4 known cryptogenes from L.tarentolae which are known to have 7 associated gRNAs. The statistical distribution of the longest gRNA when comparing random sequences is derived. Finally we develop an algorithm to search for cryptogenes using amino acid sequences from related proteins.

Algorithms↗
PubMed1987

[Computation method for optimization of recipes for protein content].

The authors propose a calculated protein utilization coefficient. This coefficient considers the difference between the utilization rates of the proteins being contained in the mixture and their amino-acid composition. The proposed formula allows calculations by computer. The data obtained show high correlations with the results received by biological tests with Tetrahymena cultures.

Amino Acids↗
PubMedDate not supplied

[Algorithms and computation methods of diagnostic coefficients in dynamic scintigraphy of skeleton and skeletal muscles].

The paper is concerned with a program for data processing of dynamic scintigraphy of the skeleton and skeletal muscles using 99mTc-sodium 1-hydroxy-ethane-1, 1-diphosphonate. Employing gamma-chamber computer the program enables rapid and precise computation of the coefficient of RP elimination from the blood and the coefficients of RP accumulation by the bones and muscle tissue. Based on those coefficients one can make diagnosis and follow the time-course of pathological changes occurring in the skeleton during endocrine diseases.

Algorithms↗