keyword
MENU ▼
Read by QxMD icon Read
search

computational structural biology

keyword
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#1
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28428742/a-set-based-mixed-effect-model-for-gene-environment-interaction-and-its-application-to-neuroimaging-phenotypes
#2
Changqing Wang, Jianping Sun, Bryan Guillaume, Tian Ge, Derrek P Hibar, Celia M T Greenwood, Anqi Qiu
Imaging genetics is an emerging field for the investigation of neuro-mechanisms linked to genetic variation. Although imaging genetics has recently shown great promise in understanding biological mechanisms for brain development and psychiatric disorders, studying the link between genetic variants and neuroimaging phenotypes remains statistically challenging due to the high-dimensionality of both genetic and neuroimaging data. This becomes even more challenging when studying gene-environment interaction (G×E) on neuroimaging phenotypes...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28427314/capturing-complexity-in-pulmonary-system-modelling
#3
Alys R Clark, Haribalan Kumar, Kelly Burrowes
Respiratory disease is a significant problem worldwide, and it is a problem with increasing prevalence. Pathology in the upper airways and lung is very difficult to diagnose and treat, as response to disease is often heterogeneous across patients. Computational models have long been used to help understand respiratory function, and these models have evolved alongside increases in the resolution of medical imaging and increased capability of functional imaging, advances in biological knowledge, mathematical techniques and computational power...
May 2017: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/28423275/single-or-multiple-access-channels-to-the-cyp450s-active-site-an-answer-from-free-energy-simulations-of-the-human-aromatase-enzyme
#4
Alessandra Magistrato, Jacopo Sgrignani, Rolf Krause, Andrea Cavalli
Cytochromes P450 (CYP450), in particular CYP19A1 and CYP17A1, are key clinical targets of breast and prostate anticancer therapies, critical players in drug metabolism and their overexpression in tumours is associated with drug resistance. In these enzymes ligands (substrates, drugs) metabolism occurs in deeply buried active sites accessible only via several gruelling channels, whose exact biological role remains unclear. Gaining direct insights on the mechanism by which ligands travel in and out, is becoming increasingly important given that channels are involved in the modulation of binding/dissociation kinetics and the specificity of ligands toward a CYP450...
April 19, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28420134/visual-detection-and-tracking-system-for-a-spherical-amphibious-robot
#5
Shuxiang Guo, Shaowu Pan, Liwei Shi, Ping Guo, Yanlin He, Kun Tang
With the goal of supporting close-range observation tasks of a spherical amphibious robot, such as ecological observations and intelligent surveillance, a moving target detection and tracking system was designed and implemented in this study. Given the restrictions presented by the amphibious environment and the small-sized spherical amphibious robot, an industrial camera and vision algorithms using adaptive appearance models were adopted to construct the proposed system. To handle the problem of light scattering and absorption in the underwater environment, the multi-scale retinex with color restoration algorithm was used for image enhancement...
April 15, 2017: Sensors
https://www.readbyqxmd.com/read/28419369/laboratory-x-ray-micro-computed-tomography-a-user-guideline-for-biological-samples
#6
Anton du Plessis, Chris Broeckhoven, Anina Guelpa, Stephan Gerhard le Roux
Laboratory X-ray micro-computed tomography (micro-CT) is a fast growing method in scientific research applications that allows for non-destructive imaging of morphological structures. This paper provides an easily operated "how-to" guide for new potential users and describes the various steps required for successful planning of research projects that involve micro-CT. Background information on micro-CT is provided, followed by relevant set-up, scanning, reconstructing and visualization methods and considerations...
April 17, 2017: GigaScience
https://www.readbyqxmd.com/read/28418199/evaluation-of-biological-activity-and-computer-aided-design-of-new-soft-glucocorticoids
#7
Vladimir Dobričić, Vesna Jaćević, Jelica Vučićević, Katarina Nikolic, Sote Vladimirov, Olivera Čudina
Soft glucocorticoids are compounds that are biotransformed to inactive and non-toxic metabolites and have fewer side effects than traditional glucocorticoids. A new class of 17β-carboxamide steroids has been recently introduced by our group. In this study, local anti-inflammatory activity of these derivatives was evaluated by use of the croton oil-induced ear edema test. Glucocorticoids with the highest maximal edema inhibition (MEI) were pointed out, and the systemic side effects of those with the lowest EC50 values were significantly lower in comparison to dexamethasone...
April 18, 2017: Archiv der Pharmazie
https://www.readbyqxmd.com/read/28417684/toward-a-multiscale-modeling-framework-for-understanding-serotonergic-function
#8
KongFatt Wong-Lin, Da-Hui Wang, Ahmed A Moustafa, Jeremiah Y Cohen, Kae Nakamura
Despite its importance in regulating emotion and mental wellbeing, the complex structure and function of the serotonergic system present formidable challenges toward understanding its mechanisms. In this paper, we review studies investigating the interactions between serotonergic and related brain systems and their behavior at multiple scales, with a focus on biologically-based computational modeling. We first discuss serotonergic intracellular signaling and neuronal excitability, followed by neuronal circuit and systems levels...
April 1, 2017: Journal of Psychopharmacology
https://www.readbyqxmd.com/read/28413234/high-dimensional-tests-for-functional-networks-of-brain-anatomic-regions
#9
Jichun Xie, Jian Kang
Exploring resting-state brain functional connectivity of autism spectrum disorders (ASD) using functional magnetic resonance imaging (fMRI) data has become a popular topic over the past few years. The data in a standard brain template consist of over 170,000 voxel specific points in time for each human subject. Such an ultra-high dimensionality makes the voxel-level functional connectivity analysis (involving four billion voxel pairs) both statistically and computationally inefficient. In this work, we introduce a new framework to identify the functional brain network at the anatomical region level for each individual...
April 2017: Journal of Multivariate Analysis
https://www.readbyqxmd.com/read/28411614/small-static-electric-field-strength-promotes-aggregation-prone-structures-in-amyloid-%C3%AE-29-42
#10
Yan Lu, Xiao-Feng Shi, Freddie R Salsbury, Philippe Derreumaux
The formation of senile plaques in central neural system resulting from the aggregation of the amyloid β (Aβ) of 40 and 42 residues is one of the two hallmarks of Alzheimer's disease. Numerous experiments and computational studies have shown that the aggregation of Aβ peptides in vitro is very complex and depends on many factors such as pH, agitation, temperature, and peptide concentration. The impact of a static electric field (EF) on amyloid peptide aggregation has been much less studied, although EFs may have some applications to treat Parkinson's disease symptoms...
April 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28410371/determining-the-role-of-missense-mutations-in-the-pou-domain-of-hnf1a-that-reduce-the-dna-binding-affinity-a-computational-approach
#11
Sneha P, Thirumal Kumar D, George Priya Doss C, Siva R, Hatem Zayed
Maturity-onset diabetes of the young type 3 (MODY3) is a non-ketotic form of diabetes associated with poor insulin secretion. Over the past years, several studies have reported the association of missense mutations in the Hepatocyte Nuclear Factor 1 Alpha (HNF1A) with MODY3. Missense mutations in the POU homeodomain (POUH) of HNF1A hinder binding to the DNA, thereby leading to a dysfunctional protein. Missense mutations of the HNF1A were retrieved from public databases and subjected to a three-step computational mutational analysis to identify the underlying mechanism...
2017: PloS One
https://www.readbyqxmd.com/read/28408471/genomes-structural-biology-and-drug-discovery-combating-the-impacts-of-mutations-in-genetic-disease-and-antibiotic-resistance
#12
REVIEW
Arun Prasad Pandurangan, David B Ascher, Sherine E Thomas, Tom L Blundell
For over four decades structural biology has been used to understand the mechanisms of disease, and structure-guided approaches have demonstrated clearly that they can contribute to many aspects of early drug discovery, both computationally and experimentally. Structure can also inform our understanding of impacts of mutations in human genetic diseases and drug resistance in cancers and infectious diseases. We discuss the ways that structural insights might be useful in both repurposing off-licence drugs and guide the design of new molecules that might be less susceptible to drug resistance in the future...
April 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28407038/emmaw-computing-minimal-absent-words-in-external-memory
#13
Alice Heliou, Solon P Pissis, Simon J Puglisi
Motivation: The biological significance of minimal absent words has been investigated in genomes of organisms from all domains of life. For instance, three minimal absent words of the human genome were found in Ebola virus genomes (Silva et al., Bioinf., 2015). There exists an O(n)-time and O(n)-space algorithm for computing all minimal absent words of a sequence of length n on a fixed-sized alphabet based on suffix arrays (Barton et al., BMC Bioinf., 2014). A standard implementation of this algorithm, when applied to a large sequence of length n, requires more than 20n bytes of RAM...
April 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28406969/reconstruction-of-3d-structures-of-met-antibodies-from-electron-microscopy-2d-class-averages
#14
Qi Chen, Michal Vieth, David E Timm, Christine Humblet, Dina Schneidman-Duhovny, Ilan E Chemmama, Andrej Sali, Wei Zeng, Jirong Lu, Ling Liu
Dynamics of three MET antibody constructs (IgG1, IgG2, and IgG4) and the IgG4-MET antigen complex was investigated by creating their atomic models with an integrative experimental and computational approach. In particular, we used two-dimensional (2D) Electron Microscopy (EM) images, image class averaging, homology modeling, Rapidly exploring Random Tree (RRT) structure sampling, and fitting of models to images, to find the relative orientations of antibody domains that are consistent with the EM images. We revealed that the conformational preferences of the constructs depend on the extent of the hinge flexibility...
2017: PloS One
https://www.readbyqxmd.com/read/28406174/complete-fold-annotation-of-the-human-proteome-using-a-novel-structural-feature-space
#15
Sarah A Middleton, Joseph Illuminati, Junhyong Kim
Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28403823/empirical-bayes-method-for-reducing-false-discovery-rates-of-correlation-matrices-with-block-diagonal-structure
#16
Clare Pacini, James W Ajioka, Gos Micklem
BACKGROUND: Correlation matrices are important in inferring relationships and networks between regulatory or signalling elements in biological systems. With currently available technology sample sizes for experiments are typically small, meaning that these correlations can be difficult to estimate. At a genome-wide scale estimation of correlation matrices can also be computationally demanding. RESULTS: We develop an empirical Bayes approach to improve covariance estimates for gene expression, where we assume the covariance matrix takes a block diagonal form...
April 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28403668/neat-flex-predicting-the-conformational-flexibility-of-amino-acids-using-neuroevolution-of-augmenting-topologies
#17
Bruno Grisci, Márcio Dorn
The development of computational methods to accurately model three-dimensional protein structures from sequences of amino acid residues is becoming increasingly important to the structural biology field. This paper addresses the challenge of predicting the tertiary structure of a given amino acid sequence, which has been reported to belong to the NP-Complete class of problems. We present a new method, namely NEAT-FLEX, based on NeuroEvolution of Augmenting Topologies (NEAT) to extract structural features from (ABS) proteins that are determined experimentally...
March 16, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28402873/saxs-oriented-ensemble-refinement-of-flexible-biomolecules
#18
Peng Cheng, Junhui Peng, Zhiyong Zhang
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28399820/multi-scale-structural-community-organisation-of-the-human-genome
#19
Rasha E Boulos, Nicolas Tremblay, Alain Arneodo, Pierre Borgnat, Benjamin Audit
BACKGROUND: Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. RESULTS: We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines...
April 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28398839/foundational-and-translational-research-opportunities-to-improve-plant-health
#20
Richard W Michelmore, Gitta Coaker, Rebecca Bart, Gwyn A Beattie, Andrew Bent, Toby Bruce, Duncan Cameron, Jeff Dangl, Savithramma Dinesh-Kumar, Robert Edwards, Sebastian Eves-van den Akker, Walter Gassmann, Jean Greenberg, Richard Harrison, Ping He, Jagger Harvey, Alisa Huffaker, Scot Hulbert, Roger Innes, Jonathan D Jones, Isgouhi Kaloshian, Sophien Kamoun, Fumiaki Katagiri, Jan E Leach, Wenbo Ma, John M McDowell, June Medford, Blake Meyers, Rebecca Nelson, Richard Peter Oliver, Yiping Qi, Diane Saunders, Michael Shaw, Prasanta Subudhi, Leslie Torrance, Brett M Tyler, John Walsh
This whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses...
April 11, 2017: Molecular Plant-microbe Interactions: MPMI
keyword
keyword
41524
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"