168 research outputs found
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Enumerating molecules.
This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz
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Developing algorithms for predicting protein-protein interactions of homology modeled proteins.
The goal of this project was to examine the protein-protein docking problem, especially as it relates to homology-based structures, identify the key bottlenecks in current software tools, and evaluate and prototype new algorithms that may be developed to improve these bottlenecks. This report describes the current challenges in the protein-protein docking problem: correctly predicting the binding site for the protein-protein interaction and correctly placing the sidechains. Two different and complementary approaches are taken that can help with the protein-protein docking problem. The first approach is to predict interaction sites prior to docking, and uses bioinformatics studies of protein-protein interactions to predict theses interaction site. The second approach is to improve validation of predicted complexes after docking, and uses an improved scoring function for evaluating proposed docked poses, incorporating a solvation term. This scoring function demonstrates significant improvement over current state-of-the art functions. Initial studies on both these approaches are promising, and argue for full development of these algorithms
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Understanding and engineering enzymes for enhanced biofuel production.
Today, carbon-rich fossil fuels, primarily oil, coal and natural gas, provide 85% of the energy consumed in the United States. The release of greenhouse gases from these fuels has spurred research into alternative, non-fossil energy sources. Lignocellulosic biomass is renewable resource that is carbon-neutral, and can provide a raw material for alternative transportation fuels. Plant-derived biomass contains cellulose, which is difficult to convert to monomeric sugars for production of fuels. The development of cost-effective and energy-efficient processes to transform the cellulosic content of biomass into fuels is hampered by significant roadblocks, including the lack of specifically developed energy crops, the difficulty in separating biomass components, the high costs of enzymatic deconstruction of biomass, and the inhibitory effect of fuels and processing byproducts on organisms responsible for producing fuels from biomass monomers. One of the main impediments to more widespread utilization of this important resource is the recalcitrance of cellulosic biomass and techniques that can be utilized to deconstruct cellulosic biomass
OVIS 3.2 user's guide.
This document describes how to obtain, install, use, and enjoy a better life with OVIS version 3.2. The OVIS project targets scalable, real-time analysis of very large data sets. We characterize the behaviors of elements and aggregations of elements (e.g., across space and time) in data sets in order to detect meaningful conditions and anomalous behaviors. We are particularly interested in determining anomalous behaviors that can be used as advance indicators of significant events of which notification can be made or upon which action can be taken or invoked. The OVIS open source tool (BSD license) is available for download at ovis.ca.sandia.gov. While we intend for it to support a variety of application domains, the OVIS tool was initially developed for, and continues to be primarily tuned for, the investigation of High Performance Compute (HPC) cluster system health. In this application it is intended to be both a system administrator tool for monitoring and a system engineer tool for exploring the system state in depth. OVIS 3.2 provides a variety of statistical tools for examining the behavior of elements in a cluster (e.g., nodes, racks) and associated resources (e.g., storage appliances and network switches). It provides an interactive 3-D physical view in which the cluster elements can be colored by raw or derived element values (e.g., temperatures, memory errors). The visual display allows the user to easily determine abnormal or outlier behaviors. Additionally, it provides search capabilities for certain scheduler logs. The OVIS capabilities were designed to be highly interactive - for example, the job search may drive an analysis which in turn may drive the user generation of a derived value which would then be examined on the physical display. The OVIS project envisions the capabilities of its tools applied to compute cluster monitoring. In the future, integration with the scheduler or resource manager will be included in a release to enable intelligent resource utilization. For example, nodes that are deemed less healthy (i.e., nodes that exhibit outlier behavior with respect to some set of variables shown to be correlated with future failure) can be discovered and assigned to shorter duration or less important jobs. Further, HPC applications with fault-tolerant capabilities would respond to changes in resource health and other OVIS notifications as needed, rather than undertaking preventative measures (e.g. checkpointing) at regular intervals unnecessarily
Tabou
Program for the fifth annual RISD Cabaret held in the Waterman Building. Design and layout by Nonie Close.https://digitalcommons.risd.edu/liberalarts_cabaret_programs/1004/thumbnail.jp
The Baryon Oscillation Spectroscopic Survey of SDSS-III
The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the
scale of baryon acoustic oscillations (BAO) in the clustering of matter over a
larger volume than the combined efforts of all previous spectroscopic surveys
of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as
i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7.
Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000
quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5.
Early results from BOSS include the first detection of the large-scale
three-dimensional clustering of the Lyman alpha forest and a strong detection
from the Data Release 9 data set of the BAO in the clustering of massive
galaxies at an effective redshift z = 0.57. We project that BOSS will yield
measurements of the angular diameter distance D_A to an accuracy of 1.0% at
redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the
same redshifts. Forecasts for Lyman alpha forest constraints predict a
measurement of an overall dilation factor that scales the highly degenerate
D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey
is complete. Here, we provide an overview of the selection of spectroscopic
targets, planning of observations, and analysis of data and data quality of
BOSS.Comment: 49 pages, 16 figures, accepted by A
Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling
The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life." While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling." This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to ellucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63164/1/153623102321112746.pd
A two-year study with cimetidine in the rat: assessment for chronic toxicity and carcinogenicity
T. F. (1981). Toxicol. Appl. PharmacoL 61, 119-137. Cimetidine [Am-cyano-N-methyl-N1-{2-[(5-methylimidazol-4-yl)methylthio]ethyl}guanidine] was administered daily for 2 years by gavage to Wistar rats at dose levels of 950, 378, and 150 mg/kg/day. Two groups, one receiving distilled wathr daily and the other not treated, served as controls. Premature deaths occurred when cimetidine was accidentally introduced into the lungs or reached the lungs by seepage from the esophagus via the larynx during intragastric administration but cimetidine treatment did not otherwise affect survival, body weight gain, clinical condition, and hematological, or urinalysis parameters. Raised transaminase levels occurred occasionally during the second year of the study in top dose males and there was a significant increase in mean liver weight in top dose females killed terminally compared with controls. Histopathological observations of the livers of these animals indicated only nonspecific changes. Mean prostate and seminal vesicle weights were significantly lower in all groups receiving cimetidine than in controls and there was dose-related atrophy of the seminiferous tubules and atrophy of the male secondary sex organs. There were no other apparent effects of treatment on nontumor pathology. Overall tumor incidence, after the exclusion of Leydig-cell tumors, was not affected by cimetidine treatment. A significantly higher incidence of benign Leydig-cell tumors in the combined cimetidine-treated groups compared with the combined control groups was confined to rats killed during Weeks 105 and 106 and was not dose related. No meaningful treatmentrelated effects on incidence were observed for any other kind of neoplasm. Cimetidine is a specific, competitive histamine H2-receptor antagonist as defined by Black et al. (1972) and is an effective inhibitor of gastric acid secretion in animals and in man. Cimetidine has been shown to have low acute toxicity and repeated dose studies of up to 12 months duration in rats and dogs have revealed no major adverse effects The present paper presents the results of a 2-year toxicity study in the rat with particular attention to incidences of neoplastic lesions
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