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A new method for calculating and displaying the molecular electrostatic potential on the molecular surface is described. The main advantage of the method, besides some others, is its consistency. This means one only needs one data set for the surface and the MEP: a 3D field of the electron density from any source.
MAIN PROBLEM: fertility data is inadequately assessed by traditional statistical methods for a variety of reasons. First, the principal test of male fertility potential, the Semen Analysis (SA) is a composite of several dissimilar parameters, and the SA and other laboratory tests of fertility potential reflect physiological mechanisms that interact in complex ways. Second, patient data is often fragmented, obtained from multiple sources. Importantly, 2 patients are required for the final result. METHODS: Novel and powerful computational method, the neural network, was explored to analyze fertility data. An integrated series of programs was written in the C computer language to implement a back propagation algorithm. A model data analysis system was chosen, predicting the penetration of zona-free hamster ova by sperm (Sperm Penetration Assay (SPA)) and the distance travelled by the farthest swimming sperm (Penetrak Assay) from the SA, for these 2 assays are generally believed by the reproductive medical community to be independent of the SA. The classification accuracy of the neural network was compared to 2 standard statistical methods, linear discriminant function analysis (LDFA) and quadratic discriminant function analysis (QDFA). RESULTS: A neural network could be trained to correctly predict the Penetrak result in over 80% of assays it had not previously encountered, and another network could predict the SPA outcome in nearly 70%. The neural network was superior to LDFA and QDFA in predicting both assay outcomes (for Penetrak: LDFA = 64%, QDFA = 69%; for SPA: LDFA = 65%, QDFA = 45%).(ABSTRACT TRUNCATED AT 250 WORDS)
Objective, computerized analysis of the maxillary arch was used for morphologic studies of cleft palate characteristics. A method for maxillary arch analysis was developed and used in 10 randomly selected, cleft palate patients. The computerized analysis procedure is described in detail.
Clinical evaluation of aortic atherosclerosis has been most commonly performed by visual analysis of aortic calcification on conventional radiographs or X-ray CT. However, precise evaluation of the degree of calcification or mild changes with increasing age can be difficult by these methods of visual analysis. A new quantitative method of evaluating the abdominal aortic atherosclerosis using CT is reported. Target CT scans of the abdominal aorta were performed at the level of the 1st, 3rd and 4th lumbar vertebrae. Two circular regions of interest (ROI) were selected along the outer margin and inner margin of the abdominal aortic wall on CT images, since it was difficult to precisely trace the aortic wall. Histograms of CT value for each pixel were made from two ROIs. A histogram at the ROI of the outer margin was depicted using class values over the maximum CT value in histogram at the ROI of inner margin which indicated flowing blood. A sum of products of the value in each class by the number in that class was divided by the aortic diameter. The value thus obtained was defined as the atherosclerotic index (S.I.). Forty-five cases were studied with this method. Six cases were excluded because of artifacts. The remaining 39 cases (16 males, 23 females) were analyzed. S.I. increased with aging and was higher in men than in women. However, it increased more rapidly in women (8.68/year) than in men (2.73/year). Because this new method employed the CT value, it is more objectively quantitative than previous methods of visual analysis in evaluating abdominal aortic atherosclerosis.(ABSTRACT TRUNCATED AT 250 WORDS)
A computational method to rapidly assess and visualize the diversity in molecular shape associated with a given compound set has been developed. Normalized ratios of principal moments of inertia are plotted into two-dimensional triangular graphs and then used to compare the shape space covered by different compound sets, such as combinatorial libraries of varying size and composition. We have further developed a computational method to analyze interset similarity in terms of shape space coverage, which allows the shape redundancy between the different subsets of a given compound collection to be analyzed in a quantitative way. The shape space coverage has been found to originate mainly from the nature and the 3D-geometry (but not the size) of the central scaffold, while the number and nature of the peripheral substituents and conformational aspects were shown to be of minor importance. Substantial shape space coverage has been correlated with broad biological activity by applying the same shape analysis to collections of known bioactive compounds, such as MDDR and the GOLD-set. The aggregate of our results corroborates the intuitive notion that molecular shape is intimately linked to biological activity and that a high degree of shape (hence scaffold) diversity in screening collections will increase the odds of addressing a broad range of biological targets.
Intracranial self-stimulation (ICSS) in the rat is a useful tool for studying the importance of various brain monoamines in positive reinforcement. The effects of compounds interacting with dopaminergic neurotransmission is measurable by studying the changes of reward thresholds. By computerisation of the analysis of these thresholds, standardisation and reproducibility is greatly enhanced. The use of an object-oriented programming language simplifies the programming of a specific application and it provides scientists without formal training in computer programming the means to create their own software. A system for the acquisition, execution, analysis and storage of ICSS experiments is described. The hardware is based on Apple Macintosh computers, interfaced to the test chambers and physiological stimulators using a plug-in card supporting A/D, D/A, digital I/O and timer functions. The software written in G (LabVIEW) provides the user with a graphically based 'Virtual Instrument' performing all aspect of the ICSS experiment. The software performs threshold analysis immediately after completion of the ICSS experiment, thereby greatly reducing the total time previously needed to evaluate these experiments. The graphical approach used in LabVIEW allows the programmer to make fast and simple alterations to suit different experimental problems.
Recently developed atomistic models of highly disordered nanoporous materials offer hope for a much more realistic description of the pore morphology and topology in such materials; however, a factor limiting their application has been the computationally intensive characterization of the models, particularly determination of the pore size distribution. We report a new technique for fast computation of pore size distributions of model materials from knowledge of the molecular coordinates. The pore size distribution (PSD) is defined as the statistical distribution of the radius of the largest sphere that can be fitted inside a pore at a given point. Using constrained nonlinear optimization, we calculate the maximum radii of test particles at random points inside the pore cavity. The final pore size distribution is then obtained by sampling the test particle radii using Monte Carlo integration. The computation time depends on factors such as the number of atoms, the sampling resolution, and the desired accuracy. However, even for large systems, PSDs with very high accuracy (>99.9%) are obtained in less than 24 h on a 3 GHz Pentium IV processor. The technique is validated by applying it to model structures, whose pore size distributions are already known. We then apply this method to investigate the pore structures of several mesoporous silica models such as SBA-15 and mesostructured cellular foams.
BACKGROUND: Many biological processes involve the physical interaction between protein domains. Understanding these functional associations requires knowledge of the molecular structure. Experimental investigations though present considerable difficulties and there is therefore a need for accurate and reliable computational methods. In this paper we present a novel method that seeks to dock protein domains using a contact map representation. Rather than providing a full three dimensional model of the complex, the method predicts contacting residues across the interface. We use a scoring function that combines structural, physicochemical and evolutionary information, where each potential residue contact is assigned a value according to the scoring function and the hypothesis is that the real configuration of contacts is the one that maximizes the score. The search is performed with a simulated annealing algorithm directly in contact space. RESULTS: We have tested the method on interacting domain pairs that are part of the same protein (intra-molecular domains). We show that it correctly predicts some contacts and that predicted residues tend to be significantly closer to each other than other pairs of residues in the same domains. Moreover we find that predicted contacts can often discriminate the best model (or the native structure, if present) among a set of optimal solutions generated by a standard docking procedure. CONCLUSION: Contact docking appears feasible and able to complement other computational methods for the prediction of protein-protein interactions. With respect to more standard docking algorithms it might be more suitable to handle protein conformational changes and to predict complexes starting from protein models.
Seryl-tRNA synthetase (SerRS) charges serine to tRNA(Ser) following the formation of a seryl adenylate intermediate, but the extent to which other non-cognate amino acids compete with serine to bind to SerRS or for the formation of the activated seryl adenylate intermediate is not known. To examine the mechanism of discrimination against non-cognate amino acids, we calculated the relative binding energies of the 20 natural amino acids to SerRS. Starting with the crystal structure of SerRS from Thermus thermophilus with seryl adenylate bound, we used the HierDock and SCREAM (Side-Chain Rotamer Energy Analysis Method) computational methods to predict the binding conformation and binding energy of each of the 20 natural amino acids in the binding site in the best-binding mode and the activating mode. The ordering of the calculated binding energies in the activated mode agrees with kinetic measurements in yeast SerRS that threonine will compete with serine for formation of the activated intermediate while alanine and glycine will not compete significantly. In addition, we predict that asparagine will compete with serine for formation of the activated intermediate. Experiments to check the accuracy of this prediction would be useful in further validating the use of HierDock and SCREAM for designing novel amino acids to incorporate into proteins and for determining mutations in aminoacyl-tRNA synthetase design to facilitate the incorporation of amino acid analogs into proteins.
The availability of high-quality molecular graphics tools in the public domain is changing the way macromolecular structure is perceived by researchers, educators and students alike. Computational methods have become increasingly important in a number of areas such as comparative or homology modelling, functional site location, characterization of ligand-binding sites in proteins, docking of small molecules into protein binding sites, protein-protein docking, and molecular dynamics simulations. The results obtained yield information that sometimes is beyond current experimental possibilities and can be used to guide and improve a vast array of experiments. On the basis of our improved level of understanding of molecular recognition and the widespread availability of target structures, it is reasonable to assume that computational methods will continue aiding not only in the design and interpretation of hypothesis-driven experiments in the field of cancer research but also in the rapid generation of new hypotheses.
Changes in arterial distensibility have been widely used to identify the presence of cardiovascular abnormalities like hypertension. Pulse wave velocity (PWV) has shown to be related to arterial distensibility. However, the lack of suitable techniques to measure PWV nonintrusively has impeded its clinical usefulness. Pulse transit time (PTT) is a noninvasive technique derived from the principle of PWV. PTT has shown its capabilities in cardiovascular and cardiorespiratory studies in adults. However, no known study has been conducted to understand the suitability and utility of PTT to estimate PWV in children. Two computational methods to derive PWV from PTT values obtained from 23 normotensive Caucasian children (19 males, aged 5-12 years old) from their finger and toe were conducted. Furthermore, the effects of adopting different postures on the PWV derivations were investigated. Statistical analyses were performed in comparison with two previous PWV studies conducted on children. Results revealed that PWV derived from the upper limb correlated significantly (P<0.05) regardless of computing methods or postures adopted. The findings here suggest that PTT measurement can be used as a convenient and noninvasive surrogate measure of derived PWV in prolonged clinical studies, especially on younger or less cooperative children. Furthermore, the simple set-up and noninvasive nature of PTT can promote its usefulness in ambulatory monitoring.
Strains of Streptococcus mutans are very susceptible to growth inhibition by benzylpenicillin, but are tolerant to lysis when exposed to even high concentrations of this drug. These properties enabled this study of S. mutans GS-5 surface growth and peptidoglycan, ribonucleic acid, protein, and deoxyribonucleic acid syntheses in the absence of osmotic stabilization. Inhibition of syntheses of peptidoglycan, ribonucleic acid, and protein was dose dependent. Synthesis of peptidoglycan was most susceptible. Substantial but less severe inhibitions of ribonucleic acid and protein syntheses rapidly followed decreased peptidoglycan synthesis, whereas inhibition of deoxyribonucleic acid synthesis was delayed and minimal. Computer-assisted reconstructions of surface growth zones and poles observed in electron micrographs of replicas were performed and indicated that at low concentrations of benzylpenicillin (0.03 micrograms/ml), growth sites reached abnormally large sizes and surface/volume ratios. The observed shifts in surface/volume ratio were attributed to an inhibition of the normal constrictive division mechanism. The poles of these cells also increased in size over those of the controls, but the relatively smaller change in surface/volume ratio confirmed the visual impression that the shape of the poles was much less altered than the shape of the growth sites. As the concentration of benzylpenicillin used was raised from 0.03 to 2 micrograms/ml, the ability of growth sites and poles to enlarge was restricted in a manner that most closely agreed with the extent of inhibition of peptidoglycan (rather than deoxyribonucleic acid, ribonucleic acid, or protein) synthesis. This correlation suggested that increases in cell size may be regulated by the supply of peptidoglycan precursors.
Fourteen fish species susceptible to substitution were analysed by the thin-layer isoelectric focusing technique on polyacrylamide gels of pH 3.5-9.5. Four fish per species were run on the same gel to verify the possibility to differentiate them according to their protein banding patterns. The occurrence of intraspecific differences due either to electrophoretic variations or to protein polymorphism was also observed. In fact, some of them showed few dissimilarities among their protein profiles. However, the differentiation was possible for all species, even for those belonging to the same order, family and genus. Computer-based tools combined with statistical analysis were implemented and usefully applied to avoid a subjective evaluation of the isoelectric focusing gels, and to verify the reliability of the preliminary visual comparison of protein patterns.
Monitoring of crystallization of calcium salts with ion-selective electrodes has turned out to be a very sensitive method. The difficulties of handling these electrodes in native whole urine and other biological fluids have been eliminated by new calcium analyzers, which clean and calibrate the electrodes after each measurement. To study crystallization kinetics, repeated calcium ion measurements have to be performed at regular intervals. For this purpose we have developed a special sampler and software. The sampler brings a thermostat-controlled crystallization chamber to the analyzer at preselected intervals. The computer directs and coordinates the sampler and the analyzer, stores the received results and prints out growth curves. Furthermore it calculates the half-time (h) and the maximum decrease of ionic calcium at infinite incubation time (delta Ca2+ infinity). Both values are shown to characterize the growth of calcium oxalate monohydrate in urine. Results are obtained within 40 min.
OBJECTIVE: To validate a menstrual symptometrics device that can quantify menstrual blood loss, dysmenorrhea, and the premenstrual syndrome against traditional methods of collecting data on symptoms. DESIGN: Validation study. SETTING: Academic research clinic for menstrual cycle disorders. PARTICIPANT(S): Women 18-50 years of age who presented with menstrual cycle disorders. Controls were recruited from lists of patients requesting sterilization and from hospital staff. INTERVENTION(S): Participants were asked to complete the menstrual symptometrics device and to record pain, blood loss, and premenstrual symptoms by using traditional methods (paper-based scales and the alkaline hematin method) for two cycles. MAIN OUTCOME MEASURE(S): Agreement between traditional methods of quantifying menstrual cycle disorders and data obtained from the menstrual symptometrics device, and acceptability of the latter technique to patients. RESULT(S): A high level of agreement was observed between the traditional methods and the menstrual symptometrics device in quantifying and diagnosing menorrhagia, dysmenorrhea, and the premenstrual syndrome. Most patients preferred the menstrual symptometrics device as a data collection tool. CONCLUSION(S): The menstrual symptometrics device is a rapid and accurate method of quantifying blood loss, pain, and premenstrual symptoms. It has a high level of patient acceptability and can provide instant pictorial feedback on symptoms for patients and clinicians.
This paper reviews recent developments by the Washington/Brown groups for the study of anatomical shape in the emerging new discipline of computational anatomy. Parametric representations of anatomical variation for computational anatomy are reviewed, restricted to the assumption of small deformations. The generation of covariance operators for probabilistic measures of anatomical variation on coordinatized submanifolds is formulated as an empirical procedure. Populations of brains are mapped to common coordinate systems, from which template coordinate systems are constructed which are closest to the population of anatomies in a minimum distance sense. Variation of several one-, two- and three-dimensional manifolds, i.e. sulci, surfaces and brain volumes are examined via Gaussian measures with mean and covariances estimated directly from maps of templates to targets. Methods are presented for estimating the covariances of vector fields from a family of empirically generated maps, posed as generalized spectrum estimation indexed over the submanifolds. Covariance estimation is made parametric, analogous to autoregressive modelling, by introducing small deformation linear operators for constraining the spectrum of the fields.
This review provides a synthesis of recent work, using computational methods, on the action and inhibition mechanisms of class I ribonucleotide reductase (RNR). This enzyme catalyzes the rate-limiting step of the pathway for the synthesis of DNA monomers and, therefore, has long been regarded as an important target for therapies aiming to control pathologies that depend strongly on DNA replication. In fact, over the last years, several molecules, which are able to impair RNR activity by different mechanisms, have been applied effectively in anti-cancer, anti-viral and anti-parasite therapies. A better understanding of the chemical mechanisms involved in normal catalysis and in inhibition of the enzyme is important for the rational design of more specific and effective inhibitor compounds. To achieve this goal, computational methods, particularly quantum chemical calculations, have been used more and more frequently. The ever-growing capabilities of these methods together with undeniable advantages make it a stimulating area for research purposes.
We have developed a computational method that detects 'identities' in tRNA genes by using principal component analysis to classify the sequences of bases in tRNA genes into groups of similar sequences and then comparing the distribution of sequences of bases, in order to extract characteristic bases that are conserved within a group but differ between groups. These classification and comparison procedures are applied recursively to classify the sequences into hierarchical groups, so that multiple levels of characteristic sites can be detected. By using this computational method, we were able to detect many characteristic sites in the T and D domains of tRNAs, as well as the characteristic sites that had already been detected experimentally. This suggests that bases not only in the contact regions but also in the elbow regions, which determine the structure and dynamics of the whole tRNA molecule, are important to the tRNA-aminoacyl tRNA synthetase recognition.