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computational structural biology

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https://www.readbyqxmd.com/read/29166560/analytical-challenges-and-recent-advances-in-mass-spectrometry-based-lipidomics
#1
Yepy Hardi Rustam, Gavin Edmund Reid
Although no internationally accepted consensus definition exists, lipids can be broadly defined as "fatty acids and their derivatives, and substances related biosynthetically or functionally to these compounds". Lipids play critical roles as (i) the major structural components of biological membranes, and as functional and regulatory components of membrane protein signaling, (ii) bioactive intra- and inter-cellular signaling molecules, and (iii) energy storage molecules for the maintenance of energy homeostasis...
November 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29166086/focused-conformational-sampling-in-proteins
#2
Marco Bacci, Cassiano Langini, Jiří Vymětal, Amedeo Caflisch, Andreas Vitalis
A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29163010/an-axiology-of-information-security-for-futuristic-neuroprostheses-upholding-human-values-in-the-context-of-technological-posthumanization
#3
Matthew E Gladden
Previous works exploring the challenges of ensuring information security for neuroprosthetic devices and their users have typically built on the traditional InfoSec concept of the "CIA Triad" of confidentiality, integrity, and availability. However, we argue that the CIA Triad provides an increasingly inadequate foundation for envisioning information security for neuroprostheses, insofar as it presumes that (1) any computational systems to be secured are merely instruments for expressing their human users' agency, and (2) computing devices are conceptually and practically separable from their users...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29161583/chrysin-sources-beneficial-pharmacological-activities-and-molecular-mechanism-of-action
#4
REVIEW
Renuka Mani, Vijayakumar Natesan
In recent years, public and scientific interest in plant flavonoids has tremendously increased because of their postulated health benefits. This review was mainly focuses on the flavone chrysin (5,7-dihydroxyflavone), which occurs naturally in many plants, honey, and propolis. A number of in vitro and in vivo studies have revealed the therapeutic effects of chrysin against various diseases. In general, chrysin exhibits many biological activities and pharmacological effects, including antioxidant, anti-inflammatory, anticancer, and antiviral activities...
November 18, 2017: Phytochemistry
https://www.readbyqxmd.com/read/29159598/etox-allies-an-automated-pipeline-for-linear-interaction-energy-based-simulations
#5
Luigi Capoferri, Marc van Dijk, Ariën S Rustenburg, Tsjerk A Wassenaar, Derk P Kooi, Eko A Rifai, Nico P E Vermeulen, Daan P Geerke
BACKGROUND: Computational methods to predict binding affinities of small ligands toward relevant biological (off-)targets are helpful in prioritizing the screening and synthesis of new drug candidates, thereby speeding up the drug discovery process. However, use of ligand-based approaches can lead to erroneous predictions when structural and dynamic features of the target substantially affect ligand binding. Free energy methods for affinity computation can include steric and electrostatic protein-ligand interactions, solvent effects, and thermal fluctuations, but often they are computationally demanding and require a high level of supervision...
November 21, 2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29158608/a-fully-coupled-space-time-multiscale-modeling-framework-for-predicting-tumor-growth
#6
Mohammad Mamunur Rahman, Yusheng Feng, Thomas E Yankeelov, J Tinsley Oden
Most biological systems encountered in living organisms involve highly complex heterogeneous multi-component structures that exhibit different physical, chemical, and biological behavior at different spatial and temporal scales. The development of predictive mathematical and computational models of multiscale events in such systems is a major challenge in contemporary computational biomechanics, particularly the development of models of growing tumors in humans. The aim of this study is to develop a general framework for tumor growth prediction by considering major biological events at tissue, cellular, and subcellular scales...
June 15, 2017: Computer Methods in Applied Mechanics and Engineering
https://www.readbyqxmd.com/read/29157200/swellix-a-computational-tool-to-explore-rna-conformational-space
#7
Nathan Sloat, Jui-Wen Liu, Susan J Schroeder
BACKGROUND: The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible non-pseudoknotted RNA structures for RNA sequences. The Swellix program builds on the Crumple program and can include experimental constraints on global RNA structures such as the minimum number and lengths of helices from crystallography, cryoelectron microscopy, or in vivo crosslinking and chemical probing methods...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29156137/biologically-consistent-annotation-of-metabolomics-data
#8
Nicholas Alden, Smitha Krishnan, Vladimir Porokhin, Ravali Raju, Kyle McElearney, Alan Gilbert, Kyongbum Lee
Annotation of metabolites remains a major challenge in liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics. The current gold standard for metabolite identification is to match the detected feature with an authentic standard analyzed on the same equipment and using the same method as the experimental samples. However, there are substantial practical challenges in applying this approach to large datasets. One widely used annotation approach is to search spectral libraries in reference databases for matching metabolites; however, this approach is limited by the incomplete coverage of these libraries...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29155564/mass-spectrometry-imaging-a-review-of-emerging-advancements-and-future-insights
#9
Amanda R Buchberger, Kellen DeLaney, Jillian Johnson, Lingjun Li
Mass spectrometry imaging (MSI) is a powerful tool that enables untargeted investigations into the spatial distribution of molecular species in a variety of samples. It has the capability to image thousands of molecules, such as metabolites, lipids, peptides, proteins, and glycans, in a single experiment without labeling. The combination of information gained from mass spectrometry (MS) and visualization of spatial distributions in thin sample sections makes this a valuable chemical analysis tool useful for biological specimen characterization...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29154867/monoamine-oxidases-inhibitors-from-colvillea-racemosa-isolation-biological-evaluation-and-computational-study
#10
Enas I Mohamed, Mohamed A Zaki, Narayan D Chaurasiya, Asmaa I Owis, Sameh AbouZid, Yan-Hong Wang, Bharathi Avula, Ahmed A Seida, Babu L Tekwani, Samir A Ross
Bioassay-guided fractionation and chemical investigation of Colvillea racemosa stems led to identification of two new α, β-dihydroxydihydrochalcones, colveol A (1) and colveol B (2) along with fifteen known compounds. The structures were elucidated via interpretation of spectroscopic data. The absolute configurations of the dihydrochalcones 1 and 2 were assigned by a combination of chemical modification and electronic circular dichroism data. The isolated compounds were evaluated for their inhibition activity toward recombinant human monoamine oxidases (rhMAO-A and -B)...
November 14, 2017: Fitoterapia
https://www.readbyqxmd.com/read/29153889/3d-qsar-studies-on-indole-and-7-azoindole-derivatives-as-rock-2-inhibitors-an-integrative-computational-approach
#11
Santhosh Kumar Nagarajan, Sathya Babu, Honglae Sohn, Panneer Devaraju, Thirumurthy Madhavan
Rho Kinases (ROCK) has been found to regulate a wide range of fundamental cell functions such as contraction, motility, proliferation, and apoptosis. Recent experiments have defined new functions of ROCKs in cells, including centrosome positioning and cell-size regulation, which might contribute to various physiological and pathological states. In this study, we have performed pharmacophore modeling and 3D QSAR studies on a series of 36 indoles and 7-azoindoles derivatives as ROCK2 inhibitors to elucidate the structural variations with their inhibitory activities...
October 9, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153737/structure-activity-relationships-and-docking-studies-of-synthetic-2-arylindole-derivatives-determined-with-aromatase-and-quinone-reductase-1
#12
Allan M Prior, Xufen Yu, Eun-Jung Park, Tamara P Kondratyuk, Yan Lin, John M Pezzuto, Dianqing Sun
In our ongoing effort of discovering anticancer and chemopreventive agents, a series of 2-arylindole derivatives were synthesized and evaluated toward aromatase and quinone reductase 1 (QR1). Biological evaluation revealed that several compounds (e.g., 2d, IC50 = 1.61 μM; 21, IC50 = 3.05 μM; and 27, IC50 = 3.34 μM) showed aromatase inhibitory activity with half maximal inhibitory concentration (IC50) values in the low micromolar concentrations. With regard to the QR1 induction activity, 11 exhibited the highest QR1 induction ratio (IR) with a low concentration to double activity (CD) value (IR = 8...
November 6, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29150680/potential-landscape-of-high-dimensional-nonlinear-stochastic-dynamics-with-large-noise
#13
Ying Tang, Ruoshi Yuan, Gaowei Wang, Xiaomei Zhu, Ping Ao
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including the cell-fate decision in developmental processes as well as the genesis and progression of cancers. While various attempts have been made to construct potential landscape in high dimensional systems and to estimate transition rates, they are practically limited to the cases where either noise is small or detailed balance condition holds. A general and practical approach to investigate real-world nonequilibrium systems, which are typically high-dimensional and subject to large multiplicative noise and the breakdown of detailed balance, remains elusive...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150626/constructing-genetic-networks-using-biomedical-literature-and-rare-event-classification
#14
Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29149552/predicting-nano-bio-interactions-by-integrating-nanoparticle-libraries-and-quantitative-nanostructure-activity-relationship-modeling
#15
Wenyi Wang, Alexander Sedykh, Hainan Sun, Linlin Zhao, Daniel P Russo, Hongyu Zhou, Bing Yan, Hao Zhu
The discovery of biocompatible or bioactive nanoparticles for medicinal applications is an expensive and time-consuming process that may be significantly facilitated by incorporating more rational approaches combining both experimental and computational methods. However, it is currently hindered by two limitations: 1) the lack of high quality comprehensive data for computational modeling, and 2) the lack of an effective modeling method for the complex nanomaterial structures. In this study, we tackled both issues by first synthesizing a large library of nanoparticles and obtained comprehensive data on their characterizations and bioactivities...
November 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/29148817/specific-recognition-of-g-quadruplexes-over-duplex-dna-by-a-macromolecular-nir-two-photon-fluorescent-probe
#16
Marco Deiana, Bastien Mettra, Lara Martinez-Fernandez, Leszek Mateusz Mazur, Krzysztof Pawlik, Chantal Andraud, Marek Samoc, Roberto Improta, Cyrille Monnereau, Katarzyna Matczyszyn
The implication of guanine-rich DNA sequences in biologically important roles such as telomerase dysfunction and the regulation of gene expression has prompted the search for structure-specific G-quadruplex agents for targeted diagnostic and therapeutic applications. To date, the number of two-photon absorbing fluorogenic dyes with intrinsically large two-photon absorption (TPA) cross-section (σ2) and quantum yield (φf), capable of specific detection of G-motifs over duplex DNAs is still limited. Herein, we report on a NIR two-photon poly(cationic) anthracene-based macromolecule able to selectively target G-quadruplexes (G4s) over genomic double-stranded DNA...
November 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29148746/keto-enol-tautomerization-triggers-an-electrophilic-aldehyde-deformylation-reaction-by-a-nonheme-manganese-iii-peroxo-complex
#17
Fabián G Cantú Reinhard, Prasenjit Barman, Gourab Mukherjee, Jitendra Kumar, Deep Kumar, Devesh Kumar, Chivukula V Sastri, Sam P de Visser
Oxygen atom transfer by high-valent enzymatic intermediates remains an enigma in chemical catalysis. In particular, manganese is an important first-row metal involved in key biochemical processes including the biosynthesis of mo-lecular oxygen (through the photosystem II complex) and biodegradation of toxic superoxide to hydrogen peroxide by superoxide dismutase. Biomimetic models of these biological systems have been developed to gain understanding on the structure and properties of short-lived intermediates but also with the aim to create environmentally benign oxidants...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29148257/multiscale-memory-and-bioelectric-error-correction-in-the-cytoplasm-cytoskeleton-membrane-system
#18
REVIEW
Chris Fields, Michael Levin
A fundamental aspect of life is the modification of anatomy, physiology, and behavior in the face of changing conditions. This is especially illustrated by the adaptive regulation of growth and form that underlies the ability of most organisms-from single cells to complex large metazoa-to develop, remodel, and regenerate to specific anatomical patterns. What is the relationship of the genome and other cellular components to the robust computations that underlie this remarkable pattern homeostasis? Here we examine the role of constraints defined at the cellular level, especially endogenous bioelectricity, in generating and propagating biological information...
November 17, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29143485/synthesis-molecular-modeling-and-biological-evaluation-of-4-5-aryl-3-thiophen-2-yl-4-5-dihydro-1h-pyrazol-1-yl-benzenesulfonamides-towards-acetylcholinesterase-carbonic-anhydrase-i-and-ii-enzymes
#19
Cem Yamali, Halise Inci Gul, Abdulilah Ece, Parham Taslimi, Ilhami Gulcin
In the present study, 4-[5-aryl-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazol-1-yl] benzenesulfonamides were synthesized and inhibition effects on AChE, hCA I and hCA II were evaluated. Ki values of the compounds towards hCA I were in the range of 24.2±4.6-49.8±12.8 nM while they were in the range of 37.3±9.0-65.3±16.7 nM towards hCA II. Ki values of the Acetazolamide were 282.1±19.7 nM and 103.60±27.6 nM towards both isoenzymes, respectively. The compounds inhibited AChE with Ki in the range of 22.7±10.3-109...
November 16, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29142788/a-unified-approach-to-model-peripheral-nerves-across-different-animal-species
#20
Elisabetta Giannessi, Maria Rita Stornelli, Pier Nicola Sergi
Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related to the nature of the external stimuli, theoretical and computational tools were used to investigate their behaviour. In this work, a Yeoh-like polynomial strain energy function was used to reproduce the response of in vitro porcine nerve. Moreover, this approach was applied to different nervous structures coming from different animal species (rabbit, lobster, Aplysia) and tested for different amount of stretch (up to extreme ones)...
2017: PeerJ
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