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PubMed2006

Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities.

UNLABELLED: RNA atomic resolution structures have revealed the existance of different families of basepair interactions, each of which with its own isosteric sub-families. Ribostral (Ribonucleic Structural Aligner) is a user-friendly framework for analyzing, evaluating and viewing RNA sequence alignments with at least one available atomic resolution structure. It is the first of its kind that makes direct and easy- to-understand superposition of the isostericity matrices of basepairs observed in the structure onto sequence alignments, easily indicating allowed and unallowed substitutions at each BP position. Potential mistakes in the alignments can then be corrected using other sequence editing software. Ribostral has been developed and tested under Windows XP, and is capable of running on any PC or MAC platform with MATLAB 7.1 (SP3) or higher installed version. A stand-alone version is also available for the PC platform. AVAILABILITY: http://rna.bgsu.edu/ribostral.

Algorithms↗
PubMed2006

COPASI--a COmplex PAthway SImulator.

MOTIVATION: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. RESULTS: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. AVAILABILITY: The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org.

Algorithms↗
PubMed2006

KGraph: a system for visualizing and evaluating complex genetic associations.

UNLABELLED: The KGraph is a data visualization system that has been developed to display the complex relationships between the univariate and bivariate associations among an outcome of interest, a set of covariates, and a set of genetic factors, such as single nucleotide polymorphisms (SNPs). It allows for easy viewing and interpretation of genetic associations, correlations among covariates and SNPs, and information about the replication and cross-validation of the associations. The KGraph allows the user to more easily investigate multicollinearity and confounding through visualization of the multidimensional correlation structure underlying genetic associations. It emphasizes gene-environment and gene-gene interaction, both important components of any genetic system that are often overlooked in association frameworks. AVAILABILITY: http://www.epidkardia.sph.umich.edu/software/kgrapher

Algorithms↗
PubMed2006

Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.

MOTIVATION: SBML is becoming a standard 'de-facto' to represent and store biological models. Although SBML is very useful in defining ways of exchanging and storing biological information, it is not formal enough to allow direct translation into non ambiguous formal representation languages to perform analysis and simulation of models. We here suggest to map SBML models into process calculi representations. RESULTS: We implemented and validated a tool that translates SBML descriptions into stochastic pi-calculus specifications. AVAILABILITY: Source code is freely available for academic use by contacting the authors.

Algorithms↗
PubMed2006

SAGA: a subgraph matching tool for biological graphs.

MOTIVATION: With the rapid increase in the availability of biological graph datasets, there is a growing need for effective and efficient graph querying methods. Due to the noisy and incomplete characteristics of these datasets, exact graph matching methods have limited use and approximate graph matching methods are required. Unfortunately, existing graph matching methods are too restrictive as they only allow exact or near exact graph matching. This paper presents a novel approximate graph matching technique called SAGA. This technique employs a flexible model for computing graph similarity, which allows for node gaps, node mismatches and graph structural differences. SAGA employs an indexing technique that allows it to efficiently evaluate queries even against large graph datasets. RESULTS: SAGA has been used to query biological pathways and literature datasets, which has revealed interesting similarities between distinct pathways that cannot be found by existing methods. These matches associate seemingly unrelated biological processes, connect studies in different sub-areas of biomedical research and thus pose hypotheses for new discoveries. SAGA is also orders of magnitude faster than existing methods. AVAILABILITY: SAGA can be accessed freely via the web at http://www.eecs.umich.edu/saga. Binaries are also freely available at this website.

Algorithms↗
PubMed2006

BioNetBuilder: automatic integration of biological networks.

UNLABELLED: BioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases. Users can create networks for approximately 1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others. The BioNetBuilder plugin client is available as a Java Webstart, providing a platform-independent network interface to these public databases. AVAILABILITY: http://err.bio.nyu.edu/cytoscape/bionetbuilder/

Algorithms↗
PubMed2006

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring.

UNLABELLED: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds the GO categories over-represented in a given network. Our plug-in, named GOlorize, first highlights the class members with category-specific color-coding and then constructs an enhanced visualization of the network using a class-directed layout algorithm. AVAILABILITY: http://www.cytoscape.org/plugins2.php. SUPPLEMENTARY INFORMATION: Installation instructions and tutorial at http://www.cytoscape.org/plugins/GOlorize/GOlorizeUserGuide.pdf.

Algorithms↗
PubMed2006

K-Fold: a tool for the prediction of the protein folding kinetic order and rate.

UNLABELLED: K-Fold is a tool for the automatic prediction of the protein folding kinetic order and rate. The tool is based on a support vector machine (SVM) that was trained on a data set of 63 proteins, whose 3D structure and folding mechanism are known from experiments already described in the literature. The method predicts whether a protein of known atomic structure folds according to a two-state or a multi-state kinetics and correctly classifies 81% of the folding mechanisms when tested over the training set of the 63 proteins. It also predicts as a further option the logarithm of the folding rate. To the best of our knowledge, the tool discriminates for the first time whether a protein is characterized by a two state or a multiple state kinetics, during the folding process, and concomitantly estimates also the value of the constant rate of the process. When used to predict the logarithm of the folding rate, K-Fold scores with a correlation value to the experimental data of 0.74 (with a SE of 1.2). AVAILABILITY: http://gpcr.biocomp.unibo.it/cgi/predictors/K-Fold/K-Fold.cgi. SUPPLEMENTARY INFORMATION: http://gpcr.biocomp.unibo.it/~emidio/K-Fold/K-Fold_help.html.

Algorithms↗
PubMed1987

7,12-Dimethylbenz[a]anthracene: refined structure, electron density distribution and endo-peroxide structure.

The crystal structure of 7,12-dimethylbenz[a]anthracene (DMBA) has been refined from new X-ray diffraction data collected at low temperature (180 K). This has allowed the location of the hydrogen atom positions not previously reported in earlier structure determinations and refinements; a more precise molecular geometry is therefore now presented. In addition, an analysis of the electron density in this carcinogenic molecule has been made by multipole refinement. These two types of studies give information on the amount of strain in the bay region and the distribution of electron density in the molecule. The molecule is highly distorted in the bay region as a result of steric overcrowding between hydrogen atoms (minimum H ... H 2.06 A) so that torsion angles of 18 degrees and 22 degrees occur in this area. The bonds in the bay region and to the two methyl groups appear to be electron-rich; however, while the K-region of DMBA has a high pi-bond density computed from interatomic distances, the multipole analysis does not indicate that it is highly electron-rich. The 7- and 12-positions (equivalent to the 9- and 10-positions of anthracene) are highly reactive and appear to show a deficiency of electron density. Molecular dioxygen can add across these positions to give a peroxy compound. The crystal structure of such an endo-peroxide of DMBA has also been studied at 180 K although not to the high precision obtained for the parent compound. Some distortions are apparent in this molecule; in particular small CH3-C-O angles (101-104 degrees) are observed, indicative of some strain in the molecule. A computer graphics analysis of the diol epoxides of DMBA, generated from X-ray coordinates of DMBA and reported values for a diol epoxide of benzo[a]pyrene, show that steric overcrowding may affect the conformation of certain isomers of the diol epoxides.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1992

Right ventricular conductance to establish closed-loop pacing.

Innovations in pacing technology, which include the addition of rate-responsive features to programmable pacemakers, can improve the quality of life of patients suffering from sick sinus syndrome. Among the strategies providing rate-adaptive cardiac pacing, the most attractive is the physiological restoration of closed-loop chronotropic control. This paper describes how autonomic nervous system (ANS) control information is extracted from dynamic measures of myocardial contractile performance obtained from unipolar conductance measurements using the stimulation electrode in the right ventricular cavity. The pacemaker uses the ANS information to modulate pacing rate and restore normal physiological control of heart rate. A new algorithm, regional effective slope quantity (RQ), for isolating the ANS signal was developed. The resulting signal, ventricular inotropic parameter (VIP), is a normalized parameter proportional to the strength of the ANS inotropic signals to the myocardium. The efficacy of the ANS control concept was evaluated in multi-centre studies. Patients with AV block and VIP-controlled pulse generators performed defined exercise protocols. The ANS-controlled pacing rate and the spontaneous sinus rate were closely correlated. Blood pressure and subjective patient reports further indicated that good control of the cardiovascular circulation was achieved.

Autonomic Nervous System↗
PubMed2006

Estimating the parameters of a model for protein-protein interaction graphs.

We find accurate approximations for the expected number of three-cycles and unchorded four-cycles under a stochastic distribution for graphs that has been proposed for modelling yeast two-hybrid protein-protein interaction networks. We show that unchorded four-cycles are characteristic motifs under this model and that the count of unchorded four-cycles in the graph is a reliable statistic on which to base parameter estimation. Finally, we test our model against a range of experimental data, obtain parameter estimates from these data and investigate possible improvements in the model. Characterization of this model lays the foundation for its use as a prior distribution in a Bayesian analysis of yeast two-hybrid networks that can potentially aid in identifying false-positive and false-negative results.

Algorithms↗
PubMed1997

Is structural flexibility of antigen-binding loops involved in the affinity maturation of anti-DNA antibodies?

Effects of somatic mutations in Ig variable region genes on the affinity maturation of autoantibodies were investigated using single precursor B cell-derived anti-double-stranded DNA mAb generated from an autoimmune disease-prone (NZB x NZW)F1 mouse. Analyses of DNA sequences, homology modeling on a graphic computer and molecular dynamics simulation of antigen-binding sites showed that any single site of mutation and changes in the electrostatic or hydrogen-bonding potential of the residues and in the three-dimensional structure could not solely explain the difference in DNA-binding activities. However, a significant increase in the flexibility of antigen-binding Fv loops, particularly VL CDR1 and VH CDR3, was associated with affinity-maturated anti-DNA antibodies. Such high flexibility of the FV loops may provide the environment where the antibodies could effectively interact with antigen DNA, a model consistent with the 'induced-fit' hypothesis of antigen-antibody interactions.

Amino Acid Sequence↗
PubMed2005

X-train: teaching professionals remotely.

Increased popularity of the Internet, along with the development of new software applications have dramatically improved our ability to create and deliver online continuing education trainings to professionals in the areas of nutrition and food safety. In addition, these technological advances permit effective and affordable measurement of training outcomes, i.e., changes in knowledge, attitude, and behavior, that result from these educational efforts. Impact assessment of engagement programs is becoming increasing important for demonstrating the value of training activities to stakeholders. A novel software program, called X-Train, takes advantage of technological advances (databases, computer graphics, Web-based interfaces, and network speed) for delivering high-quality trainings to teachers and health care professionals. X-Train automatically collects outcome data, and generates and sends certificates of completion and communicates with participants through electronic messages. X-Train can be used as a collaborative tool whereby experts from various academic institutions are brought together to develop Web-based trainings. Finally, X-Train uses a unique approach that encourages cooperative extension specialists and educators to promote these educational opportunities within their state or county.

Dietary Supplements↗
PubMed2006

3D lidar imaging for detecting and understanding plant responses and canopy structure.

Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

Biosensing Techniques↗
PubMed1986

Secondary structure of Tetrahymena thermophilia 5S ribosomal RNA as revealed by enzymatic digestion and microdensitometric analysis.

The secondary structure of [32P] end-labeled 5S rRNA from Tetrahymena thermophilia (strain B) has been investigated using the enzymes S1 nuclease, cobra venom ribonuclease and T2 ribonuclease. The results, analyzed by scanning microdensitometry and illustrated by three-dimensional computer graphics, support the secondary structure model of Curtiss and Vournakis for 5S rRNA. Aberrent mobility of certain RNA fragments on sequencing gels was observed as regions of band compression. These regions are postulated to be caused by stable internal base-pairing. The molecule was probed with T2 RNase in neutral (pH 7.5) and acidic (pH 4.5) buffers and only minor structural differences were revealed. One of the helices was found to be susceptible to enzymatic attack by both the single-strand and double-strand specific enzymes. These observations are evidence for the existence of dynamic structural equilibria in 5S rRNA.

Densitometry↗
PubMed1990

Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model.

The solution structure of human U1 snRNA was investigated by using base-specific chemical probes (dimethylsulfate, carbodiimide, diethylpyrocarbonate) and RNase V1. Chemical reagents were employed under various conditions of salt and temperature and allowed information at the Watson-Crick base-pairing positions to be obtained for 66% of the U1 snRNA bases. Double-stranded or stacked regions were examined with RNase V1. The dat gained from these experiments extend and support the previous 2D model for U1snRNA. However, to elucidate some aspects of the solution data that could not be accounted for by the secondary structure model, the information gathered from structure probing was used to provide the experimental basis required to construct and to test a tertiary structure model by computer graphics modeling. As a result, U1 snRNA is shown to adopt an asymmetrical X-shape that is formed by two helical domains, each one being generated by coaxial stacking of helices at the U1 snRNA cruciform. Chemical reactivities and model building show that a few nucleotides, previously proposed to be unpaired, can form A.G and U.U non Watson-Crick base-pairs, notably in stem-loop B. The structural model we propose for regions G12 to A124 integrates stereochemical constraints and is based both on solution structure data and sequence comparisons between U1 snRNAs.

Alkylating Agents↗
PubMed1997

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.

Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here we describe a program called NUCPLOT which can automatically identify these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows all the interactions in a schematic manner. The program produces a PostScript output file representing hydrogen, van der Waals and covalent bonds between the protein and the DNA. The resulting diagram is both clear and simple and allows immediate identification of important interactions within the structure. It also facilitates comparison of binding found in different structures. NUCPLOT is a completely automatic program, which can be used for any protein-DNA complex and will also work for certain protein-RNA structures.

Computer Graphics↗