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computational structural biology

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https://www.readbyqxmd.com/read/29351988/confirmation-of-intersubunit-connectivity-and-topology-of-designed-protein-complexes-by-native-ms
#1
Aniruddha Sahasrabuddhe, Yang Hsia, Florian Busch, William Sheffler, Neil P King, David Baker, Vicki H Wysocki
Computational protein design provides the tools to expand the diversity of protein complexes beyond those found in nature. Understanding the rules that drive proteins to interact with each other enables the design of protein-protein interactions to generate specific protein assemblies. In this work, we designed protein-protein interfaces between dimers and trimers to generate dodecameric protein assemblies with dihedral point group symmetry. We subsequently analyzed the designed protein complexes by native MS...
January 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29351266/from-extraction-of-local-structures-of-protein-energy-landscapes-to-improved-decoy-selection-in-template-free-protein-structure-prediction
#2
Nasrin Akhter, Amarda Shehu
Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging...
January 19, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29347715/cusps-enable-line-attractors-for-neural-computation
#3
Zhuocheng Xiao, Jiwei Zhang, Andrew T Sornborger, Louis Tao
Line attractors in neuronal networks have been suggested to be the basis of many brain functions, such as working memory, oculomotor control, head movement, locomotion, and sensory processing. In this paper, we make the connection between line attractors and pulse gating in feed-forward neuronal networks. In this context, because of their neutral stability along a one-dimensional manifold, line attractors are associated with a time-translational invariance that allows graded information to be propagated from one neuronal population to the next...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29344895/bioinformatics-approaches-to-predict-drug-responses-from-genomic-sequencing
#4
Neel S Madhukar, Olivier Elemento
Fulfilling the promises of precision medicine will depend on our ability to create patient-specific treatment regimens. Therefore, being able to translate genomic sequencing into predicting how a patient will respond to a given drug is critical. In this chapter, we review common bioinformatics approaches that aim to use sequencing data to predict sample-specific drug susceptibility. First, we explain the importance of customized drug regimens to the future of medical care. Second, we discuss the different public databases and community efforts that can be leveraged to develop new methods for identifying new predictive biomarkers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29340790/an-automated-framework-for-qsar-model-building
#5
Samina Kausar, Andre O Falcao
BACKGROUND: In-silico quantitative structure-activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules based on their chemical structure. With the passage of time, the exponentially growing amount of synthesized and known chemicals data demands computationally efficient automated QSAR modeling tools, available to researchers that may lack extensive knowledge of machine learning modeling...
January 16, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29340616/pychimera-use-ucsf-chimera-modules-in-any-python-2-7-project
#6
Jaime Rodríguez-Guerra Pedregal, Jean-Didier Maréchal
Motivation: UCSF Chimera (Pettersen et al., 2004) is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C ++ core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera's arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX (Goddard et al...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29338468/inhibition-of-the-proteasome-activity-by-graphene-oxide-contributes-to-its-cytotoxicity
#7
Xiaochuan Ma, Sangyun Lee, Xingshu Fei, Ge Fang, Tien Huynh, Yu Chong, Zhifang Chai, Cuicui Ge, Ruhong Zhou
Due to its hydrophobicity and other unique physicochemical properties, graphene oxide (GO) has been extensively utilized in various biological applications. However, introducing nanomaterials into the biological environment may raise serious risk in terms of nanotoxicity, leading to some unintended changes to the structure and the function of other biomolecules. This study investigates the interaction of GO with the ubiquitin-proteasome system, one of the essential machineries in the cellular metabolism, using a combination of experimental and computational approaches...
January 16, 2018: Nanotoxicology
https://www.readbyqxmd.com/read/29338454/chemical-computational-and-functional-insights-into-the-chemical-stability-of-the-hedgehog-pathway-inhibitor-gant61
#8
Andrea Calcaterra, Valentina Iovine, Bruno Botta, Deborah Quaglio, Ilaria D'Acquarica, Alessia Ciogli, Antonia Iazzetti, Romina Alfonsi, Ludovica Lospinoso Severini, Paola Infante, Lucia Di Marcotullio, Mattia Mori, Francesca Ghirga
This work aims at elucidating the mechanism and kinetics of hydrolysis of GANT61, the first and most-widely used inhibitor of the Hedgehog (Hh) signalling pathway that targets Glioma-associated oncogene homologue (Gli) proteins, and at confirming the chemical nature of its bioactive form. GANT61 is poorly stable under physiological conditions and rapidly hydrolyses into an aldehyde species (GANT61-A), which is devoid of the biological activity against Hh signalling, and a diamine derivative (GANT61-D), which has shown inhibition of Gli-mediated transcription...
December 2018: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/29336153/a-genetic-algorithm-based-design-and-experimental-characterization-of-a-highly-thermostable-metalloprotein
#9
Esra Bozkurt, Marta A S Perez, Ruud Hovius, Nicholas J Browning, Ursula Rothlisberger
The development of thermostable and solvent-tolerant metalloproteins is a long-sought goal for many applications in synthetic biology and biotechnology. In this work, we were able to engineer a highly thermo- and organic solvent-stable metallo variant of the B1 domain of protein G (GB1) with a tetrahedral zinc-binding site reminiscent of the one of ther-molysin. Promising candidates were designed computationally by applying a protocol based on classical and first-principles molecular dynamics simulations in combination with genetic algorithm (GA) optimization...
January 16, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29334891/tuning-iteration-space-slicing-based-tiled-multi-core-code-implementing-nussinov-s-rna-folding
#10
Marek Palkowski, Wlodzimierz Bielecki
BACKGROUND: RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding...
January 15, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29329461/high-heritability-of-adolescent-sleep-wake-behavior-on-free-but-not-school-days-a-long-term-twin-study
#11
A P Inderkum, L Tarokh
Adolescence development is characterized by significant changes in sleep biology. Despite an overall decline in sleep duration and a delay in bedtime, significant inter-individual variation in sleep has been reported. The aim of the current study was to examine genetic and environmental influences on sleep in adolescence using long-term (6-month) actigraphy measurements, differentiating between school and free days. Sixteen monozygotic (MZ; n = 32) and 10 dizygotic (DZ; n = 20) twin pairs (mean age 12.8 ± 1...
January 10, 2018: Sleep
https://www.readbyqxmd.com/read/29329283/modeling-the-assembly-order-of-multimeric-heteroprotein-complexes
#12
Lenna X Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly...
January 12, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29328962/so-you-think-computational-approaches-to-understanding-glycosaminoglycan-protein-interactions-are-too-dry-and-too-rigid-think-again
#13
REVIEW
Nehru Viji Sankaranarayanan, Balaji Nagarajan, Umesh R Desai
Glycosaminoglycans (GAGs) play key roles in virtually all biologic responses through their interaction with proteins. A major challenge in understanding these roles is their massive structural complexity. Computational approaches are extremely useful in navigating this bottleneck and, in some cases, the only avenue to gain comprehensive insight. We discuss the state-of-the-art on computational approaches and present a flowchart to help answer most basic, and some advanced, questions on GAG-protein interactions...
January 9, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29328623/mimicking-biological-synaptic-functionality-with-an-indium-phosphide-synaptic-device-on-silicon-for-scalable-neuromorphic-computing
#14
Debarghya Sarkar, Jun Tao, Wei Wang, Qingfeng Lin, Matthew Yeung, Chenhao Ren, Rehan Kapadia
Neuromorphic or "brain-like" computation is a leading candidate for efficient, fault-tolerant processing of large-scale data, as well as real-time sensing and transduction of complex multivariate systems and networks such as self-driving vehicles or Internet of Things applications. In biology, the synapse serves as an active memory unit in the neural system, and is the component responsible for learning and memory. Electronically emulating this element via a compact, scalable technology which can be integrated in a 3-D architecture is critical for future implementations of neuromorphic processors...
January 12, 2018: ACS Nano
https://www.readbyqxmd.com/read/29324364/automatic-non-invasive-heartbeat-quantification-of-drosophila-pupae
#15
Dimitri Berh, Aaron Scherzinger, Nils Otto, Xiaoyi Jiang, Christian Klämbt, Benjamin Risse
The importance of studying model organisms such as Drosophila melanogaster has significantly increased in recent biological research. Amongst others, Drosophila can be used to study heart development and heartbeat related diseases. Here we propose a method for automatic in vivo heartbeat detection of Drosophila melanogaster pupae based on morphological structures which are recorded without any dissection using FIM imaging. Our approach is easy-to-use, has low computational costs, and enables high-throughput experiments...
December 29, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29323726/computational-chemical-biology-and-drug-design-facilitating-protein-structure-function-and-modulation-studies
#16
REVIEW
Mingyue Zheng, Jihui Zhao, Chen Cui, Zunyun Fu, Xutong Li, Xiaohong Liu, Xiaoyu Ding, Xiaoqin Tan, Fei Li, Xiaomin Luo, Kaixian Chen, Hualiang Jiang
Over the past quarter of a century, there has been rapid development in structural biology, which now can provide solid evidence for understanding the functions of proteins. Concurrently, computational approaches with particular relevance to the chemical biology and drug design (CBDD) field have also incrementally and steadily improved. Today, these methods help elucidate detailed working mechanisms and accelerate the discovery of new chemical modulators of proteins. In recent years, integrating computational simulations and predictions with experimental validation has allowed for more effective explorations of the structure, function and modulation of important therapeutic targets...
January 11, 2018: Medicinal Research Reviews
https://www.readbyqxmd.com/read/29322925/subtype-identification-from-heterogeneous-tcga-datasets-on-a-genomic-scale-by-multi-view-clustering-with-enhanced-consensus
#17
Menglan Cai, Limin Li
BACKGROUND: The Cancer Genome Atlas (TCGA) has collected transcriptome, genome and epigenome information for over 20 cancers from thousands of patients. The availability of these diverse data types makes it necessary to combine these data to capture the heterogeneity of biological processes and phenotypes and further identify homogeneous subtypes for cancers such as breast cancer. Many multi-view clustering approaches are proposed to discover clusters across different data types. The problem is challenging when different data types show poor agreement of clustering structure...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29318379/osteoinduction-and-conduction-through-absorbable-bone-substitute-materials-based-on-calcium-sulfate-in-vivo-biological-behavior-in-a-rabbit-model
#18
D Pförringer, N Harrasser, H Mühlhofer, M Kiokekli, A Stemberger, M van Griensven, M Lucke, R Burgkart, A Obermeier
Calcium sulfate (CS) can be used as an antibiotically impregnated bone substitute in a variety of clinical constellations. Antibiotically loaded bone substitutes find specific application in orthopedic and trauma surgery to prevent or treat bone infections especially in relation to open bone defects. However, its use as a structural bone graft reveals some concerns due to its fast biodegradation. The addition of calcium carbonate and tripalmitin makes CS formulations more resistant to resorption leaving bone time to form during a prolonged degradation process...
January 9, 2018: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/29318304/prediction-of-physico-chemical-properties-of-bacteriostatic-n1-substituted-sulfonamides-theoretical-and-experimental-studies
#19
Hossein Nikoofard, Mohsen Sargolzaei, Farnosh Faridbod
A computational study at the density functional theory (DFT) as well as electrochemical methods, was carried out on the structural and physico-chemical properties of a series of sulfonamide derivatives (SAs) as WHO essential medications in the treatment of basic health system. The B3LYP/6-311++G(d,p) level of theory carried out on sulfadiazine (SDZ), sulfathiazole (STZ), sulfaquinoxaline (SQX), sulfacetamide (SAA), and the reference unsubstituted sulfonamide (SA) was discussed and rationalized in term of the N1-sulfonamide substituent...
December 2017: Acta Chimica Slovenica
https://www.readbyqxmd.com/read/29316260/genetic-origin-and-dispersal-of-the-invasive-soybean-aphid-inferred-from-population-genetic-analysis-and-approximate-bayesian-computation
#20
Fang Fang, Jing Chen, Li-Yun Jiang, Yan-Hua Qu, Ge-Xia Qiao
Biological invasion is considered one of the most important global environmental problems. Knowledge of the source and dispersal routes of invasion could facilitate the eradication and control of invasive species. Soybean aphid, Aphis glycines Matsumura, is one of the most destructive soybean pests. For effective management of this pest, we conducted genetic analyses and approximate Bayesian computation (ABC) analysis to determine the origins and dispersal of the aphid species, as well as the source of its invasion in the USA, using eight microsatellite loci and the mitochondrial cytochrome c oxidase subunit I (COI) gene...
January 9, 2018: Integrative Zoology
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