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computational structural biology

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https://www.readbyqxmd.com/read/29793060/a-computational-framework-for-the-detection-of-subcortical-brain-dysmaturation-in-neonatal-mri-using-3d-convolutional-neural-networks
#1
Rafael Ceschin, Alexandria Zahner, William Reynolds, Jenna Gaesser, Giulio Zuccoli, Cecilia W Lo, Vanathi Gopalakrishnan, Ashok Panigrahy
Deep neural networks are increasingly being used in both supervised learning for classification tasks and unsupervised learning to derive complex patterns from the input data. However, the successful implementation of deep neural networks using neuroimaging datasets requires adequate sample size for training and well-defined signal intensity based structural differentiation. There is a lack of effective automated diagnostic tools for the reliable detection of brain dysmaturation in the neonatal period, related to small sample size and complex undifferentiated brain structures, despite both translational research and clinical importance...
May 21, 2018: NeuroImage
https://www.readbyqxmd.com/read/29792707/nano-scale-conductive-filament-with-alternating-rectification-as-an-artificial-synapse-building-block
#2
Dan Berco, Yu Zhou, Sankara Rao Gollu, Pranav Sairam Kalaga, Abhisek Kole, Mohamed Hassan, Diing Shenp Ang
A popular approach for resistive memory (RRAM) based hardware implementation of neural networks utilizes one (or two) device that functions as an analog synapse in a crossbar structure of perpendicular pre- and post-synaptic neurons. An ideal fully automated, large scale artificial neural network, that matches a biologic counterpart (in terms of density and energy consumption), thus requires nano sized, extremely low power devices with a wide dynamic range and multi level functionality. Unfortunately the tradeoff between these traits proves to be a serious obstacle in the realization of brain inspired computing platforms yet to be overcome...
May 24, 2018: ACS Nano
https://www.readbyqxmd.com/read/29790909/ebic-an-evolutionary-based-parallel-biclustering-algorithm-for-pattern-discovery
#3
Patryk Orzechowski, Moshe Sipper, Xiuzhen Huang, Jason H Moore
Motivation: Biclustering algorithms are commonly used for gene expression data analysis. However, accurate identification of meaningful structures is very challenging and state-of-the-art methods are incapable of discovering with high accuracy different patterns of high biological relevance. Results: In this paper a novel biclustering algorithm based on evolutionary computation, a subfield of artificial intelligence (AI), is introduced. The method called EBIC aims to detect order-preserving patterns in complex data...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790754/epiprofile-2-0-a-computational-platform-for-processing-epi-proteomics-mass-spectrometry-data
#4
Zuo-Fei Yuan, Simone Sidoli, Dylan M Marchione, Johayra Simithy, Kevin A Janssen, Mary R Szurgot, Benjamin A Garcia
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here, we present EpiProfile 2.0, an extended version of our 2015 software (v1.0) for accurate quantification of histone peptides based on liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29789473/effect-of-sewage-irrigation-on-the-ct-measured-soil-pore-characteristics-of-a-clay-farmland-in-northern-china
#5
Xiaoming Guo, Tongqian Zhao, Lin Liu, Chunyan Xiao, Yuxiao He
Sewage irrigation has a strong influence on the physical, chemical, and biological properties of soil. However, the effects of sewage irrigation on the pore characteristics of soil are not well understood. This study compares the effects of sewage irrigation and groundwater irrigation on computed tomography (CT)-measured pore parameters and examines the relationships between CT-measured pore parameters and soil physicochemical and microbial properties. Intact soil cores were collected from S1 irrigated with sewage for 25 years, S2 irrigated with sewage for 52 years, and CK irrigated with groundwater...
May 22, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29788889/targeting-key-transporters-in-tumor-glycolysis-as-a-novel-anticancer-strategy
#6
Yunli Shi, Shengnan Liu, Shabir Ahmad, Qingzhi Gao
Increased glycolysis has been one of the metabolic characteristics known as the Warburg effect. The functional and therapeutic importance of the Warburg effect in targeted therapy is scientifically recognized and the glucose metabolic pathway has become a desirable target of anticancer strategies. Glucose transporters (GLUTs) play an important role in cancer glycolysis to sustain cancer cell proliferation, metastasis and survival. Utilizing the knowledge of differential expression and biological functions of GLUTs offers us the possibility of designing and delivering chemotherapeutics toward targeted tumor tissues for improved cancer selectivity...
May 22, 2018: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29788355/swiss-model-homology-modelling-of-protein-structures-and-complexes
#7
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli, Rosalba Lepore, Torsten Schwede
Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29787971/cellular-mechanisms-of-physicochemical-membrane-homeostasis
#8
REVIEW
Robert Ernst, Stephanie Ballweg, Ilya Levental
Biological membranes are vital, active contributors to cell function. In addition to specific interactions of individual lipid molecules and lateral organization produced by membrane domains, the bulk physicochemical properties of biological membranes broadly regulate protein structure and function. Therefore, these properties must be homeostatically maintained within a narrow range that is compatible with cellular physiology. Although such adaptiveness has been known for decades, recent observations have dramatically expanded its scope by showing the breadth of membrane properties that must be maintained, and revealing the remarkable diversity of biological membranes, both within and between cell types...
May 19, 2018: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/29785930/shearing-in-flow-environment-promotes-evolution-of-social-behavior-in-microbial-populations
#9
Gurdip Uppal, Dervis Vural
How producers of public goods persist in microbial communities is a major question in evolutionary biology. Cooperation is evolutionarily unstable, since cheating strains can reproduce quicker and take over. Spatial structure has been shown to be a robust mechanism for the evolution of cooperation. Here we study how spatial assortment might emerge from native dynamics and show that fluid flow shear promotes cooperative behavior. Social structures arise naturally from our advection-diffusion-reaction model as self-reproducing Turing patterns...
May 22, 2018: ELife
https://www.readbyqxmd.com/read/29784056/biomarker-micrornas-for-prostate-cancer-metastasis-screened-with-a-network-vulnerability-analysis-model
#10
Yuxin Lin, Feifei Chen, Li Shen, Xiaoyu Tang, Cui Du, Zhandong Sun, Huijie Ding, Jiajia Chen, Bairong Shen
BACKGROUND: Prostate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases. METHODS: In this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis...
May 21, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29782151/a-computational-workflow-for-the-automated-generation-of-models-of-genetic-designs
#11
Göksel Mısırlı, Tramy Nguyen, James Alastair McLaughlin, Prashant Vaidyanathan, Timothy Jones, Douglas Densmore, Chris J Myers, Anil Wipat
Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modelling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models has still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards...
May 21, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29775059/intrinsic-antioxidant-potential-of-the-aminoindole-structure-a-computational-kinetics-study-of-tryptamine
#12
Erika N Bentz, Rosana Maria Lobayan, Henar Martinez, Pilar Redondo, Antonio Largo
A computational kinetics study of the antioxidant activity of tryptamine toward HO● and HOO● radicals in water at 298 K has been carried out. Density functional methods have been employed for the quantum chemical calculations and conventional transition state theory was used for rate constants evaluation. Different mechanisms have been considered: radical adduct formation (RAF), single electron transfer (SET), and hydrogen atom transfer (HAT). For the reaction of tryptamine with the hydroxyl radical nearly all channels are diffusion controlled, and the overall rate constant is very high, 6...
May 18, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29771985/another-cat-and-mouse-game-deciphering-the-evolution-of-the-scgb-superfamily-and-exploring-the-molecular-similarity-of-major-cat-allergen-fel-d-1-and-mouse-abp-using-computational-approaches
#13
Rajesh Durairaj, Patrick Pageat, Cécile Bienboire-Frosini
The mammalian secretoglobin (SCGB) superfamily contains functionally diverse members, among which the major cat allergen Fel d 1 and mouse salivary androgen-binding protein (ABP) display similar subunits. We searched for molecular similarities between Fel d 1 and ABP to examine the possibility that they play similar roles. We aimed to i) cluster the evolutionary relationships of the SCGB superfamily; ii) identify divergence patterns, structural overlap, and protein-protein docking between Fel d 1 and ABP dimers; and iii) explore the residual interaction between ABP dimers and steroid binding in chemical communication using computational approaches...
2018: PloS One
https://www.readbyqxmd.com/read/29762023/reinforced-adversarial-neural-computer-for-de-novo-molecular-design
#14
Evgeny Putin, Arip Asadulaev, Yan Ivanenkov, Vladimir Aladinskiy, Benjamin Sánchez-Lengeling, Alán Aspuru-Guzik, Alex Zhavoronkov
In silico modeling is a crucial milestone in modern drug design & development. Although computer-aided approaches in this field are well-studied, the application of deep learning methods in this research area is at the beginning. In this work, we present an original deep neural network (DNN) architecture named RANC (Reinforced Adversarial Neural Computer) for the de novo design of novel small-molecule organic structures based on generative adversarial network (GAN) paradigm and reinforcement learning (RL)...
May 15, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29760975/high-throughput-intensity-diffraction-tomography-with-a-computational-microscope
#15
Ruilong Ling, Waleed Tahir, Hsing-Ying Lin, Hakho Lee, Lei Tian
We demonstrate a motion-free intensity diffraction tomography technique that enables the direct inversion of 3D phase and absorption from intensity-only measurements for weakly scattering samples. We derive a novel linear forward model featuring slice-wise phase and absorption transfer functions using angled illumination. This new framework facilitates flexible and efficient data acquisition, enabling arbitrary sampling of the illumination angles. The reconstruction algorithm performs 3D synthetic aperture using a robust computation and memory efficient slice-wise deconvolution to achieve resolution up to the incoherent limit...
May 1, 2018: Biomedical Optics Express
https://www.readbyqxmd.com/read/29756279/designed-enzyme-promotes-selective-post-translational-acylation
#16
Pallavi Gosavi, Megha Jayachandran, Joel Rempillo, Oleksii Zozulia, Olga Makhlyents, Ivan Korendovych
A computationally designed allosterically regulated catalyst (CaM M144H) produced by substituting a single residue in calmodulin, a non-enzymatic protein, is capable of efficient and site selective post-translational acylation of lysines in peptides with highly diverse sequences. Calmodulin binding partners are involved in regulating a large number of cellular processes, this new chemical biology tool will help identify them and provide structural insight into their interactions with calmodulin.
May 13, 2018: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29755970/how-to-achieve-better-results-using-pass-based-virtual-screening-case-study-for-kinase-inhibitors
#17
Pavel V Pogodin, Alexey A Lagunin, Anastasia V Rudik, Dmitry A Filimonov, Dmitry S Druzhilovskiy, Mark C Nicklaus, Vladimir V Poroikov
Discovery of new pharmaceutical substances is currently boosted by the possibility of utilization of the Synthetically Accessible Virtual Inventory (SAVI) library, which includes about 283 million molecules, each annotated with a proposed synthetic one-step route from commercially available starting materials. The SAVI database is well-suited for ligand-based methods of virtual screening to select molecules for experimental testing. In this study, we compare the performance of three approaches for the analysis of structure-activity relationships that differ in their criteria for selecting of "active" and "inactive" compounds included in the training sets...
2018: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29755750/ionic-scattering-factors-of-atoms-that-compose-biological-molecules
#18
Koji Yonekura, Rei Matsuoka, Yoshiki Yamashita, Tsutomu Yamane, Mitsunori Ikeguchi, Akinori Kidera, Saori Maki-Yonekura
Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac-Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O- . Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology...
May 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29755507/computational-protein-phenotype-characterization-of-il10ra-mutations-causative-to-early-onset-inflammatory-bowel-disease-ibd
#19
Fahad A Al-Abbasi, Kaleemuddin Mohammed, Saida Sadath, Babajan Banaganapalli, Khalidah Nasser, Noor A Shaik
The deleterious amino acid substitution mutations in IL-10 receptor alpha gene are most frequently reported in several autoimmune diseases including early onset-inflammatory bowel disease (IBD). Despite the important role of IL-10 RA in maintaining immune homeostasis, the specific structural and functional implications of these mutations on protein phenotype, stability, ligand binding and post translational characteristics is not well explored. Therefore, this study performed the multidimensional computational analysis of IL10RA missense variations causative to pediatric or early onset inflammatory bowel disease (<5 years of age)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29755311/interactive-sonification-exploring-emergent-behavior-applying-models-for-biological-information-and-listening
#20
Insook Choi
Sonification is an open-ended design task to construct sound informing a listener of data. Understanding application context is critical for shaping design requirements for data translation into sound. Sonification requires methodology to maintain reproducibility when data sources exhibit non-linear properties of self-organization and emergent behavior. This research formalizes interactive sonification in an extensible model to support reproducibility when data exhibits emergent behavior. In the absence of sonification theory, extensibility demonstrates relevant methods across case studies...
2018: Frontiers in Neuroscience
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