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Refinement validation structure

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https://www.readbyqxmd.com/read/28422350/electronic-g-tensors-in-u-v-complexes-a-computational-study
#1
Helen Moylan, Joseph McDouall
The theory and computation of EPR parameters from first principles has seen a great deal of development over the past two decades. In particular, various techniques for the computation of the electronic g tensor have been implemented in many quantum chemistry packages. These methods have been successfully applied to paramagnetic organic species and transition metal systems. The situation is less well-understood and established in the case of actinide containing molecules and there is a dearth of experimental data available for validation of computations...
April 19, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28419717/ligand-recognition-properties-of-the-vasopressin-v2-receptor-studied-under-qsar-and-molecular-modeling-strategies
#2
Marlet Martínez-Archundia, Brenda Colín-Astudillo, L M Moreno-Vargas, G Ramírez-Galicia, R Garduño-Juárez, O Deeb, Martha C Contreras-Romo, A Quintanar-Stephano, Edgar Abarca-Rojano, José Correa-Basurto
The design of new drugs that target vasopressin 2 receptor (V2R) is of vital importance to develop new therapeutic alternatives to treat diseases such as heart failure, polycystic kidney disease, etc. To get structural insights related to V2R-ligand recognition, we have used a combined approach of docking, molecular dynamics simulations (MD) and quantitative structure-activity relationship (QSAR) to elucidate the detailed interaction of the V2R with 119 of its antagonists. The three-dimensional model of V2R was built by threading methods refining its structure through MD simulations upon which the 119 ligands were subjected to docking studies...
April 17, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28413366/organizational-context-and-capabilities-for-integrating-care-a-framework-for-improvement
#3
Jenna M Evans, Agnes Grudniewicz, G Ross Baker, Walter P Wodchis
BACKGROUND: Interventions aimed at integrating care have become widespread in healthcare; however, there is significant variability in their success. Differences in organizational contexts and associated capabilities may be responsible for some of this variability. PURPOSE: This study develops and validates a conceptual framework of organizational capabilities for integrating care, identifies which of these capabilities may be most important, and explores the mechanisms by which they influence integrated care efforts...
August 31, 2016: International Journal of Integrated Care
https://www.readbyqxmd.com/read/28412404/development-of-human-biotransformation-qsars-and-application-for-pbt-assessment-refinement
#4
Ester Papa, Alessandro Sangion, Jon A Arnot, Paola Gramatica
Toxicokinetics heavily influence chemical toxicity as the result of Absorption, Distribution, Metabolism (Biotransformation) and Elimination (ADME) processes. Biotransformation (metabolism) reactions can lead to detoxification or, in some cases, bioactivation of parent compounds to more toxic chemicals. Moreover, biotransformation has been recognized as a key process determining chemical half-life in an organism and is thus a key determinant for bioaccumulation assessment for many chemicals. This study addresses the development of QSAR models for the prediction of in vivo whole body human biotransformation (metabolism) half-lives measured or empirically-derived for over 1000 chemicals, mainly represented by pharmaceuticals...
April 13, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28407140/development-and-testing-of-candidate-items-for-inclusion-in-a-new-rheumatoid-arthritis-stiffness-patient-reported-outcome-measure
#5
Serena Halls, Emma Dures, John R Kirwan, Jon Pollock, Gill Baker, Avis Edmunds, Sarah Hewlett
Objective.: To qualitatively develop and test a set of candidate items for a new RA stiffness patient-reported outcome measure (PROM) that capture the patient perspective. This is an essential first step in PROM development, prior to quantitative development, assessment and validation. Methods.: Focus groups further examined the previously developed stiffness conceptual model and explored the patient perspective regarding stiffness assessment. Data were analysed using thematic analysis...
April 11, 2017: Rheumatology
https://www.readbyqxmd.com/read/28402873/saxs-oriented-ensemble-refinement-of-flexible-biomolecules
#6
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/28398748/polarizable-force-field-for-dna-based-on-the-classical-drude-oscillator-ii-microsecond-molecular-dynamics-simulations-of-duplex-dna
#7
Justin A Lemkul, Alexander D MacKerell
The structure and dynamics of DNA are governed by a sensitive balance between base stacking and pairing, hydration, and interactions with ions. Force-field models that include explicit representations of electronic polarization are capable of more accurately modeling the subtle details of these interactions versus commonly used additive force fields. In this work, we validate our recently refined polarizable force field for DNA based on the classical Drude oscillator model, in which electronic degrees of freedom are represented as negatively charged particles attached to their parent atoms via harmonic springs...
April 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28393677/in-silico-high-throughput-virtual-screening-and-molecular-dynamics-simulation-study-to-identify-inhibitor-for-adeabc-efflux-pump-of-acinetobacter-baumannii
#8
Privita Verma, Monalisa Tiwari, Vishvanath Tiwari
Emergence of multi-drug resistant strains of Acinetobacter baumannii has caused significant health problems and is responsible for high morbidity and mortality. Overexpression of AdeABC efflux system is one of the major mechanisms. In this study, we have focused on overcoming the drug resistance by identifying inhibitors that can effectively bind and inhibit integral membrane protein, AdeB of this efflux pump. We performed homology modeling to generate structure of AdeB using MODELLER v9.16 followed by model refinement using 3D-Refine tool and validated using PSVS, ProsaWeb, ERRAT etc...
April 10, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28389892/in-silico-identification-and-validation-of-a-novel-hypothetical-protein-in-cryptosporidium-hominis-and-virtual-screening-of-inhibitors-as-therapeutics
#9
Arpit Kumar Shrivastava, Subrat Kumar, Priyadarshi Soumyaranjan Sahu, Rajani Kanta Mahapatra
Computational approaches to predict structure/function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are ineffective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines...
April 7, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28383703/mcsm-na-predicting-the-effects-of-mutations-on-protein-nucleic-acids-interactions
#10
Douglas E V Pires, David B Ascher
Over the past two decades, several computational methods have been proposed to predict how missense mutations can affect protein structure and function, either by altering protein stability or interactions with its partners, shedding light into potential molecular mechanisms giving rise to different phenotypes. Effectively and efficiently predicting consequences of mutations on protein-nucleic acid interactions, however, remained until recently a great and unmet challenge. Here we report an updated webserver for mCSM-NA, the only scalable method we are aware of capable of quantitatively predicting the effects of mutations in protein coding regions on nucleic acid binding affinities...
April 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28376110/3d-membrane-segmentation-and-quantification-of-intact-thick-cells-using-cryo-soft-x-ray-transmission-microscopy-a-pilot-study
#11
Rubén Cárdenes, Chong Zhang, Oxana Klementieva, Stephan Werner, Peter Guttmann, Christoph Pratsch, Josep Cladera, Bart H Bijnens
Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state...
2017: PloS One
https://www.readbyqxmd.com/read/28376062/axial-spondyloarthritis-classification-criteria-the-debate-continues
#12
Maureen Dubreuil, Atul Deodhar
PURPOSE OF REVIEW: The Assessment of Spondyloarthritis International Society (ASAS) axial spondyloarthritis (axSpA) classification criteria marked a major step forward in SpA research, distinguishing axial from peripheral disease, and allowing earlier identification through MRI. This facilitated all aspects of research including epidemiology, therapeutics and patient outcomes. RECENT FINDINGS: The ASAS axSpA classification criteria have been applied broadly in research, and were validated in a recent meta-analysis of international studies...
April 3, 2017: Current Opinion in Rheumatology
https://www.readbyqxmd.com/read/28375143/data-mining-of-iron-ii-and-iron-iii-bond-valence-parameters-and-their-relevance-for-macromolecular-crystallography
#13
Heping Zheng, Karol M Langner, Gregory P Shields, Jing Hou, Marcin Kowiel, Frank H Allen, Garib Murshudov, Wladek Minor
The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R0 parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal-organic bond-valence parameters...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28368827/brane-clust-cluster-assisted-gene-regulatory-network-inference-refinement
#14
Aurelie Pirayre, Camille Couprie, Laurent Duval, Jean-Christophe Pesquet
Discovering meaningful gene interactions is crucial for the identification of novel regulatory processes in cells. Building accurately the related graphs remains challenging due to the large number of possible solutions from available data. Nonetheless, enforcing a priori on the graph structure, such as modularity, may reduce network indeterminacy issues. BRANE Clust (Biologically-Related A priori Network Enhancement with Clustering) refines gene regulatory network (GRN) inference thanks to cluster information...
March 28, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28367461/analyzing-the-curriculum-of-the-faculty-of-medicine-university-of-gezira-using-harden-s-10-questions-framework
#15
Yasar Albushra Ahmed, Salma Alneel
INTRODUCTION: Despite the importance of curriculum analysis for internal refinement of a programme, the approach for such a step in under-described in the literature. This article describes the analysis of the medical curriculum at the Faculty of Medicine, University of Gezira (FMUG). This analysis is crucial in the era of innovative medical education since introducing new curricula and curricular changes has become a common occurrence in medical education worldwide. METHODS: The curriculum analysis was qualitatively approached using descriptive analysis and adopting Harden's 10 Questions of curriculum development framework approach...
April 2017: Journal of Advances in Medical Education & Professionalism
https://www.readbyqxmd.com/read/28345622/comprehensive-track-structure-based-evaluation-of-dna-damage-by-light-ions-from-radiotherapy-relevant-energies-down-to-stopping
#16
W Friedland, E Schmitt, P Kundrát, M Dingfelder, G Baiocco, S Barbieri, A Ottolenghi
Track structures and resulting DNA damage in human cells have been simulated for hydrogen, helium, carbon, nitrogen, oxygen and neon ions with 0.25-256 MeV/u energy. The needed ion interaction cross sections have been scaled from those of hydrogen; Barkas scaling formula has been refined, extending its applicability down to about 10 keV/u, and validated against established stopping power data. Linear energy transfer (LET) has been scored from energy deposits in a cell nucleus; for very low-energy ions, it has been defined locally within thin slabs...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#17
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28341584/development-of-videogrammetry-as-a-tool-for-gas-particle-fluidization-research
#18
S Anweiler
Many industries use fluidization of solid particles for energy efficiency or environmental friendly process development, and this paper introduces research techniques developed for investigating gas-particle systems At present there is plenty of room for refining gas-particle fluidization process. With the rapidly rising application of mathematical modelling, real time visualization of processes will be widely used for validation of those models in the near future. In presented research, photogrammetry, as a part of close range vision metrology, has been expanded to allow dynamic space and time analysis of the phase concentration distribution inside fluidization devices...
March 21, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28319851/-31-p-dephased-13-c-detected-redor-for-nmr-crystallography-at-natural-isotopic-abundance
#19
Alexander I Greenwood, Mary C Clay, Chad M Rienstra
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one...
February 28, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28291758/using-more-than-801%C3%A2-296-small-molecule-crystal-structures-to-aid-in-protein-structure-refinement-and-analysis
#20
Jason C Cole, Ilenia Giangreco, Colin R Groom
The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal-organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein-ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
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