5,705 research outputs found
The benefits of in silico modeling to identify possible small-molecule drugs and their off-target interactions
Accepted for publication in a future issue of Future Medicinal Chemistry.The research into the use of small molecules as drugs continues to be a key driver in the development of molecular databases, computer-aided drug design software and collaborative platforms. The evolution of computational approaches is driven by the essential criteria that a drug molecule has to fulfill, from the affinity to targets to minimal side effects while having adequate absorption, distribution, metabolism, and excretion (ADME) properties. A combination of ligand- and structure-based drug development approaches is already used to obtain consensus predictions of small molecule activities and their off-target interactions. Further integration of these methods into easy-to-use workflows informed by systems biology could realize the full potential of available data in the drug discovery and reduce the attrition of drug candidates.Peer reviewe
Crowdsourcing Swarm Manipulation Experiments: A Massive Online User Study with Large Swarms of Simple Robots
Micro- and nanorobotics have the potential to revolutionize many applications
including targeted material delivery, assembly, and surgery. The same
properties that promise breakthrough solutions---small size and large
populations---present unique challenges to generating controlled motion. We
want to use large swarms of robots to perform manipulation tasks;
unfortunately, human-swarm interaction studies as conducted today are limited
in sample size, are difficult to reproduce, and are prone to hardware failures.
We present an alternative.
This paper examines the perils, pitfalls, and possibilities we discovered by
launching SwarmControl.net, an online game where players steer swarms of up to
500 robots to complete manipulation challenges. We record statistics from
thousands of players, and use the game to explore aspects of large-population
robot control. We present the game framework as a new, open-source tool for
large-scale user experiments. Our results have potential applications in human
control of micro- and nanorobots, supply insight for automatic controllers, and
provide a template for large online robotic research experiments.Comment: 8 pages, 13 figures, to appear at 2014 IEEE International Conference
on Robotics and Automation (ICRA 2014
InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.
Phasing of single nucleotide (SNV), and structural variations into chromosome-wide haplotypes in humans has been challenging, and required either trio sequencing or restricting phasing to population-based haplotypes. Selvaraj et al demonstrated single individual SNV phasing is possible with proximity ligated (HiC) sequencing. Here, we demonstrate HiC can phase structural variants into phased scaffolds of SNVs. Since HiC data is noisy, and SV calling is challenging, we applied a range of supervised classification techniques, including Support Vector Machines and Random Forest, to phase deletions. Our approach was demonstrated on deletion calls and phasings on the NA12878 human genome. We used three NA12878 chromosomes and simulated chromosomes to train model parameters. The remaining NA12878 chromosomes withheld from training were used to evaluate phasing accuracy. Random Forest had the highest accuracy and correctly phased 86% of the deletions with allele-specific read evidence. Allele-specific read evidence was found for 76% of the deletions. HiC provides significant read evidence for accurately phasing 33% of the deletions. Also, eight of eight top ranked deletions phased by only HiC were validated using long range polymerase chain reaction and Sanger. Thus, deletions from a single individual can be accurately phased using a combination of shotgun and proximity ligation sequencing. InPhaDel software is available at: http://l337x911.github.io/inphadel/
ARL3 mutations cause Joubert syndrome by disrupting ciliary protein composition
Joubert syndrome (JBTS) is a genetically heterogeneous autosomal recessive neurodevelopmental
ciliopathy. We investigated further the underlying genetic etiology of Joubert syndrome by studying
two unrelated families in whom JBTS was not associated with pathogenic variants in known JBTSrelated
genes. Combined autozygosity mapping of both families highlighted a candidate locus on
chromosome 10 (chr10: 101569997-109106128 (hg 19)), and exome sequencing revealed two
missense variants in ARL3 within the candidate locus. The encoded protein, ADP Ribosylation
Factor-Like GTPase 3, ARL3, is a small GTP-binding protein that is involved in directing lipid-modified
proteins into the cilium in a GTP-dependent manner. Both missense variants replace the highly
conserved Arg149 residue, which we show to be necessary for the interaction with its guanine
nucleotide exchange factor ARL13B, such that the mutant protein is associated with reduced INPP5E
and NPHP3 localisation in cilia. We propose that ARL3 provides a potential hub in the network of
encoded ciliopathy genes, whereby perturbation of ARL3 results in the mislocalisation of multiple
ciliary proteins due to abnormal displacement of lipidated protein cargo
COEL: A Web-based Chemistry Simulation Framework
The chemical reaction network (CRN) is a widely used formalism to describe
macroscopic behavior of chemical systems. Available tools for CRN modelling and
simulation require local access, installation, and often involve local file
storage, which is susceptible to loss, lacks searchable structure, and does not
support concurrency. Furthermore, simulations are often single-threaded, and
user interfaces are non-trivial to use. Therefore there are significant hurdles
to conducting efficient and collaborative chemical research. In this paper, we
introduce a new enterprise chemistry simulation framework, COEL, which
addresses these issues. COEL is the first web-based framework of its kind. A
visually pleasing and intuitive user interface, simulations that run on a large
computational grid, reliable database storage, and transactional services make
COEL ideal for collaborative research and education. COEL's most prominent
features include ODE-based simulations of chemical reaction networks and
multicompartment reaction networks, with rich options for user interactions
with those networks. COEL provides DNA-strand displacement transformations and
visualization (and is to our knowledge the first CRN framework to do so), GA
optimization of rate constants, expression validation, an application-wide
plotting engine, and SBML/Octave/Matlab export. We also present an overview of
the underlying software and technologies employed and describe the main
architectural decisions driving our development. COEL is available at
http://coel-sim.org for selected research teams only. We plan to provide a part
of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl
Data analysis and navigation in high-dimensional chemical and biological spaces
The goal of this master thesis is to develop and validate a visual data-mining
approach suitable for the screening of chemicals in the context of REACH [Registration, Evaluation, Authorization and
Restriction of Chemicals]. The
proposed approach will facilitate the development and validation of non-testing
methods via the exploration of environmental endpoints and their relationship with
the chemical structure and physicochemical properties of chemicals.
The use of an interactive chemical space data exploration tool using 3D visualization
and navigation will enrich the information available with additional variables like
size, texture and color of the objects of the scene (compounds). The features that
distinguish this approach and make it unique are (i) the integration of multiple data
sources allowing the recovery in real time of complementary information of the
studied compounds, (ii) the integration of several algorithms for the data analysis
(dimensional reduction, generation of composite variables and clustering) and (iii)
direct user interaction with the data through the virtual navigation mechanism. All
this is achieved without the need for specialized hardware or the use of specific
devices and high-cost virtual reality and mixed reality
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