A computational method to characterize framework aluminum in aluminosilicates.
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Aluminum↗
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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↗
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↗
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↗
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↗
A computer method of shield construction for extended fields irradiation of Hodgkin's disease.
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Computers↗
Comparison of computational methods for the identification of cell cycle-regulated genes.
MOTIVATION: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been subjected to a wide range of bioinformatics analysis methods, aimed at identifying the correct and complete set of periodically expressed genes. RESULTS: Here, we provide the first thorough benchmark of such methods, surprisingly revealing that most new and more mathematically advanced methods actually perform worse than the analysis published with the original microarray data sets. We show that this loss of accuracy specifically affects methods that only model the shape of the expression profile without taking into account the magnitude of regulation. We present a simple permutation-based method that performs better than most existing methods.
Algorithms↗
A computed method for noninvasive MRI assessment of pulmonary arterial hypertension.
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Humans↗
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↗
Hydrodynamic models and computational methods for NMR relaxation.
Interpretation of NMR relaxation data of macromolecules is based on the analysis of their dynamic behavior in solution. For quasirigid molecules, in addition to a minor, separable contribution from local mobility, the main contribution corresponds to the overall rotational diffusion of the complete molecule. Therefore, theoretical descriptions and computational methodologies for hydrodynamic calculations, which yield the full, anisotropic rotational diffusion tensor of rigid molecules, are extremely helpful in the analysis of NMR relaxation. Recent approaches allow realistic predictions of the rotational diffusion tensor from structures at atomic detail. This enables measured relaxation rates and structural models to be compared. Such a comparison (1) provides an independent test of the structural model, (2) provides a framework for the interpretation of local motion, even for highly anisotropic systems, (3) provides a simple method for the detection of additional sources of relaxation, such as chemical exchange, and (4) provides a sensitive method for the detection of nonspecific aggregation or oligomer formation. Although hydrodynamic calculations usually assume a rigid structure, Brownian dynamics simulations extend their range of applications to flexible multidomain structures. Hydrodynamic applications are not restricted to globular proteins. Small DNA fragments, which could be otherwise considered cylindrical objects, can also be treated with atomic detail using the same methodology used for proteins.
Computational Biology↗
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↗
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↗
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↗
[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↗
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry.
The combined method of LC-MS/MS is increasingly being used to explore differences in the proteomic composition of complex biological systems. The reliability and utility of such comparative protein expression profiling studies is critically dependent on an accurate and rigorous assessment of quantitative changes in the relative abundance of the myriad of proteins typically present in a biological sample such as blood or tissue. In this review, we provide an overview of key statistical and computational issues relevant to bottom-up shotgun global proteomic analysis, with an emphasis on methods that can be applied to improve the dependability of biological inferences drawn from large proteomic datasets. Focusing on a start-to-finish approach, we address the following topics: 1) low-level data processing steps, such as formation of a data matrix, filtering, and baseline subtraction to minimize noise, 2) mid-level processing steps, such as data normalization, alignment in time, peak detection, peak quantification, peak matching, and error models, to facilitate profile comparisons; and, 3) high-level processing steps such as sample classification and biomarker discovery, and related topics such as significance testing, multiple testing, and choice of feature space. We report on approaches that have recently been developed for these steps, discussing their merits and limitations, and propose areas deserving of further research.
Animals↗
[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↗
[Computer methods of data processing in clinical electro- encephalography (review of the literature)].
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Action Potentials↗
Structural polymorphism of the HIV-1 leader region explored by computational methods.
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5'-untranslated leader region (5'-UTR) can fold in vitro into two alternative conformations, branched (BMH) and 'linearized' (LDI) and switch between them to achieve different functionality. In this study we computationally explored in detail, with our massively parallel genetic algorithm (MPGAfold), the propensity of 13 HIV-1 5'-UTRs to fold into the BMH and the LDI conformation types. Besides the BMH conformations these results predict the existence of two functionally equivalent types of LDI conformations. One is similar to what has been shown in vitro to exist in HIV-1 LAI, the other is a novel conformation exemplified by HIV-1 MAL long-distance interactions. These novel MPGAfold results are further corroborated by a consensus probability matrix algorithm applied to a set of 155 HIV-1 sequences. We also have determined in detail the impact of various strain mutations, domain sizes and folds of elongating sequences simulating folding during transcription on HIV-1 RNA secondary structure folding dynamics.
5' Untranslated Regions↗