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computational structural biology

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https://www.readbyqxmd.com/read/28944079/quantitative-systems-biology-to-decipher-design-principles-of-a-dynamic-cell-cycle-network-the-maximum-allowable-mammalian-trade-off-weight-mamtow
#1
REVIEW
Matteo Barberis, Paul Verbruggen
Network complexity is required to lend cellular processes flexibility to respond timely to a variety of dynamic signals, while simultaneously warranting robustness to protect cellular integrity against perturbations. The cell cycle serves as a paradigm for such processes; it maintains its frequency and temporal structure (although these may differ among cell types) under the former, but accelerates under the latter. Cell cycle molecules act together in time and in different cellular compartments to execute cell type-specific programs...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28943294/nested-positive-feedback-loops-in-the-maintenance-of-major-depression-an-integration-and-extension-of-previous-models
#2
REVIEW
Ryan Smith, Anna Akozei, William D S Killgore, Richard D Lane
Several theories of Major Depressive Disorder (MDD) have previously been proposed, focusing largely on either a psychological (i.e., cognitive/affective), biological, or neural/computational level of description. These theories appeal to somewhat distinct bodies of work that have each highlighted separate factors as being of considerable potential importance to the maintenance of MDD. Such factors include a range of cognitive/attentional information-processing biases, a range of structural and functional brain abnormalities, and also dysregulation within the autonomic, endocrine, and immune systems...
September 21, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28938868/start-a-system-for-flexible-analysis-of-hundreds-of-genomic-signal-tracks-in-few-lines-of-sql-like-queries
#3
Xinjie Zhu, Qiang Zhang, Eric Dun Ho, Ken Hung-On Yu, Chris Liu, Tim H Huang, Alfred Sze-Lok Cheng, Ben Kao, Eric Lo, Kevin Y Yip
BACKGROUND: A genomic signal track is a set of genomic intervals associated with values of various types, such as measurements from high-throughput experiments. Analysis of signal tracks requires complex computational methods, which often make the analysts focus too much on the detailed computational steps rather than on their biological questions. RESULTS: Here we propose Signal Track Query Language (STQL) for simple analysis of signal tracks. It is a Structured Query Language (SQL)-like declarative language, which means one only specifies what computations need to be done but not how these computations are to be carried out...
September 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28937982/protein-complex-prediction-via-dense-subgraphs-and-false-positive-analysis
#4
Cecilia Hernandez, Carlos Mella, Gonzalo Navarro, Alvaro Olivera-Nappa, Jaime Araya
Many proteins work together with others in groups called complexes in order to achieve a specific function. Discovering protein complexes is important for understanding biological processes and predict protein functions in living organisms. Large-scale and throughput techniques have made possible to compile protein-protein interaction networks (PPI networks), which have been used in several computational approaches for detecting protein complexes. Those predictions might guide future biologic experimental research...
2017: PloS One
https://www.readbyqxmd.com/read/28937298/probing-the-toxicity-of-nanoparticles-a-unified-in-silico-machine-learning-model-based-on-perturbation-theory
#5
Riccardo Concu, Valeria V Kleandrova, Alejandro Speck-Planche, M Natália D S Cordeiro
Nanoparticles (NPs) are part of our daily life, having a wide range of applications in engineering, physics, chemistry, and biomedicine. However, there are serious concerns regarding the harmful effects that NPs can cause to the different biological systems and their ecosystems. Toxicity testing is an essential step for assessing the potential risks of the NPs, but the experimental assays are often very expensive and usually too slow to flag the number of NPs that may cause adverse effects. In silico models centered on quantitative structure-activity/toxicity relationships (QSAR/QSTR) are alternative tools that have become valuable supports to risk assessment, rationalizing the search for safer NPs...
September 22, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/28934693/enzyme-classification-using-multiclass-support-vector-machine-and-feature-subset-selection
#6
Debasmita Pradhan, Sudarsan Padhy, Biswajit Sahoo
Proteins are the macromolecules responsible for almost all biological processes in a cell. With the availability of large number of protein sequences from different sequencing projects, the challenge with the scientist is to characterize their functions. As the wet lab methods are time consuming and expensive, many computational methods such as FASTA, PSI-BLAST, DNA microarray clustering, and Nearest Neighborhood classification on protein-protein interaction network have been proposed. Support vector machine is one such method that has been used successfully for several problems such as protein fold recognition, protein structure prediction etc...
August 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28934478/tuning-rna-folding-and-function-through-rational-design-of-junction-topology
#7
May Daher, Anthony M Mustoe, Alex Morriss-Andrews, Charles L Brooks Iii, Nils G Walter
Structured RNAs such as ribozymes must fold into specific 3D structures to carry out their biological functions. While it is well-known that architectural features such as flexible junctions between helices help guide RNA tertiary folding, the mechanisms through which junctions influence folding remain poorly understood. We combine computational modeling with single molecule Förster resonance energy transfer (smFRET) and catalytic activity measurements to investigate the influence of junction design on the folding and function of the hairpin ribozyme...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934236/automated-computer-assisted-quantitative-analysis-of-intact-murine-lungs-at-the-alveolar-scale
#8
Goran Lovric, Ioannis Vogiatzis Oikonomidis, Rajmund Mokso, Marco Stampanoni, Matthias Roth-Kleiner, Johannes C Schittny
Using state-of-the-art X-ray tomographic microscopy we can image lung tissue in three dimensions in intact animals down to a micrometer precision. The structural complexity and hierarchical branching scheme of the lung at this level of details, however, renders the extraction of biologically relevant quantities particularly challenging. We have developed a methodology for a detailed description of lung inflation patterns by measuring the size and the local curvature of the parenchymal airspaces. These quantitative tools for morphological and topological analyses were applied to high-resolution murine 3D lung image data, inflated at different pressure levels under immediate post mortem conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28933304/survey-of-predictors-of-propensity-for-protein-production-and-crystallization-with-application-to-predict-resolution-of-crystal-structures
#9
Jian-Zhao Gao, Zhonghua Wu, Gang Hu, Kui Wang, Jiangning Song, Andrzej Joachimiak, Lukasz Kurgan
Selection of proper targets for the X-ray crystallography will benefit biological research community immensely. Several computational models were proposed to predict propensity of successful protein production and diffraction quality crystallization from protein sequences. We reviewed a comprehensive collection of 22 such predictors that were developed in the last decade. We found that almost all of these models are easily accessible as webservers and/or standalone software and we demonstrated that some of them are widely used by the research community...
September 20, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28927929/mechanical-characterization-of-structurally-porous-biomaterials-built-via-additive-manufacturing-experiments-predictive-models-and-design-maps-for-load-bearing-bone-replacement-implants
#10
D Melancon, Z S Bagheri, R B Johnston, L Liu, M Tanzer, D Pasini
Porous biomaterials can be additively manufactured with micro-architecture tailored to satisfy the stringent mechano-biological requirements imposed by bone replacement implants. In a previous investigation, we introduced structurally porous biomaterials, featuring strength five times stronger than commercially available porous materials, and confirmed their bone ingrowth capability in an in-vivo canine model. While encouraging, the manufactured biomaterials showed geometric mismatches between their internal porous architecture and that of its as-designed counterpart, as well as discrepancies between predicted and tested mechanical properties, issues not fully elucidated...
September 16, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28925954/quantitative-structure-activity-relationship-modeling-of-kinase-selectivity-profiles
#11
Sandeepkumar Kothiwale, Corina Borza, Ambra Pozzi, Jens Meiler
The discovery of selective inhibitors of biological target proteins is the primary goal of many drug discovery campaigns. However, this goal has proven elusive, especially for inhibitors targeting the well-conserved orthosteric adenosine triphosphate (ATP) binding pocket of kinase enzymes. The human kinome is large and it is rather difficult to profile early lead compounds against around 500 targets to gain an upfront knowledge on selectivity. Further, selectivity can change drastically during derivatization of an initial lead compound...
September 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28920628/fluoroquinolones-as-imaging-agents-for-bacterial-infection
#12
Syed Ali Raza Naqvi, Karl Drlica
Diagnosis of deep-seated bacterial infection is difficult, as neither standard anatomical imaging nor radiolabeled, autologous leukocytes distinguish sterile inflammation from infection. Two recent imaging efforts are receiving attention: (1) radioactive derivatives of sorbitol show good specificity with Gram-negative bacterial infections, and (2) success in combining anatomical and functional imaging for cancer diagnosis has rekindled interest in (99m)Tc-fluoroquinolone-based imaging. With the latter, computed tomography (CT) would be combined with single-photon-emission-computed tomography (SPECT) to detect (99m)Tc-fluoroquinolone-bacterial interactions...
September 18, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28917842/multi-scale-simulations-of-biological-systems-using-the-opep-coarse-grained-model
#13
Fabio Sterpone, Sébastien Doutreligne, Thanh Thuy Tran, Simone Melchionna, Marc Baaden, Phuong H Nguyen, Philippe Derreumaux
Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28915752/a-new-insight-into-diffusional-escape-from-a-biased-cylindrical-trap
#14
Alexander M Berezhkovskii, Leonardo Dagdug, Sergey M Bezrukov
Recent experiments with single biological nanopores, as well as single-molecule fluorescence spectroscopy and pulling studies of protein and nucleic acid folding raised a number of questions that stimulated theoretical and computational investigations of barrier crossing dynamics. The present paper addresses a closely related problem focusing on trajectories of Brownian particles that escape from a cylindrical trap in the presence of a force F parallel to the cylinder axis. To gain new insights into the escape dynamics, we analyze the "fine structure" of these trajectories...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28913654/discriminating-cirrnas-from-other-lncrnas-using-a-hierarchical-extreme-learning-machine-h-elm-algorithm-with-feature-selection
#15
Lei Chen, Yu-Hang Zhang, Guohua Huang, Xiaoyong Pan, ShaoPeng Wang, Tao Huang, Yu-Dong Cai
As non-coding RNAs, circular RNAs (cirRNAs) and long non-coding RNAs (lncRNAs) have attracted an increasing amount of attention. They have been confirmed to participate in many biological processes, including playing roles in transcriptional regulation, regulating protein-coding genes, and binding to RNA-associated proteins. Until now, the differences between these two types of non-coding RNAs have not been fully uncovered. It is still quite difficult to detect cirRNAs from other lncRNAs using simple techniques...
September 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28910090/improved-accuracy-for-constant-ph-remd-simulations-through-modification-of-carboxylate-effective-radii
#16
Andrew Vincent Yeager, Jason M Swails, Bill Ray Miller Iii
The accuracy of computational models for simulating biomolecules in specific solution pH conditions is critical for properly representing the effect of pH in biological processes. Constant pH (CpH) simulations involving implicit solvent using the AMBER software often incorrectly estimate pKa values of aspartate and glutamate residues due to large effective radii stemming from the presence of dummy protons. These inaccuracies stem from problems in the sampled ensembles of titratable residues that can influence other observable pH-dependent behavior, such as conformational change...
September 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28905911/the-4d-nucleome-project
#17
Job Dekker, Andrew S Belmont, Mitchell Guttman, Victor O Leshyk, John T Lis, Stavros Lomvardas, Leonid A Mirny, Clodagh C O'Shea, Peter J Park, Bing Ren, Joan C Ritland Politz, Jay Shendure, Sheng Zhong
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28905390/validation-of-the-gatortail-method-for-accurate-sizing-of-pulmonary-vessels-from-3d-medical-images
#18
Walter G O'Dell, Anne K Gormaley, David A Prida
PURPOSE: Detailed characterization of changes in vessel size is crucial for the diagnosis and management of a variety of vascular diseases. Because clinical measurement of vessel size is typically dependent on the radiologist's subjective interpretation of the vessel borders, it is often prone to high inter- and intra-user variability. Automatic methods of vessel sizing have been developed for two-dimensional images but a fully three-dimensional (3D) method suitable for vessel sizing from volumetric X-ray computed tomography (CT) or magnetic resonance imaging has heretofore not been demonstrated and validated robustly...
September 14, 2017: Medical Physics
https://www.readbyqxmd.com/read/28900011/robust-mechanobiological-behavior-emerges-in-heterogeneous-myosin-systems
#19
Paul F Egan, Jeffrey R Moore, Allen J Ehrlicher, David A Weitz, Christian Schunn, Jonathan Cagan, Philip LeDuc
Biological complexity presents challenges for understanding natural phenomenon and engineering new technologies, particularly in systems with molecular heterogeneity. Such complexity is present in myosin motor protein systems, and computational modeling is essential for determining how collective myosin interactions produce emergent system behavior. We develop a computational approach for altering myosin isoform parameters and their collective organization, and support predictions with in vitro experiments of motility assays with α-actinins as molecular force sensors...
September 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28899099/accurately-modeling-the-conformational-preferences-of-nucleosides
#20
Mihai Burai Patrascu, Elise Malek-Adamian, Masad J Damha, Nicolas Moitessier
Sugar puckering of nucleosides impacts nucleic acid structures; hence their biological function. Similarly, nucleoside-based therapeutics may adopt different conformations affecting their binding affinity, DNA incorporation, and excision rates. As a result, significant efforts have been made to develop nucleoside analogues adopting specific conformations to improve bioactivity and pharmacokinetic profiles of the corresponding nucleoside-containing drugs. Understanding and ultimately predicting these conformational preferences would significantly help in the design of more effective structures...
September 25, 2017: Journal of the American Chemical Society
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