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https://www.readbyqxmd.com/read/28533339/structure-based-prediction-of-wnt-binding-affinities-for-frizzled-type-cysteine-rich-domain
#1
Mark Agostino, Sebastian Öther-Gee Pohl, Arunasalam Dharmarajan
Wnt signaling pathways are of significant interest in development and oncogenesis. The first step in these pathways typically involves the binding of a Wnt protein to the cysteine-rich domain (CRD) of a Frizzled receptor; Wnt-Frizzled interactions can be antagonized by secreted Frizzled-related proteins (sFRPs), which also contain a Frizzled-like CRD. The large number of Wnts, Frizzleds and sFRPs, as well as the hydrophobic nature of Wnt, pose challenges to laboratory-based investigations of interactions involving Wnt...
May 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28523927/retinoid-bms411-4-5-5-dimethyl-8-phenyl-5-6-dihydronaphthalen-2-yl-carbonyl-amino-benzoic-acid-a-potential-inhibitor-of-ns5a-protein-of-hepatitis-c-virus-a-candidate-for-combined-therapy-of-hepatitis-c-infection
#2
S Ibrahim, M J Asad, R T Mahmood, F H Wattoo, S Akhter, D Shahwar
Hepatitis C infection is a serious health issue worldwide caused by hepatitis C virus (HCV). There is an urgent need of search for new direct acting antiviral drugs due to the rapid development of drug resistance. The HCV NS5A protein is involved in creating resistance against antiviral therapy and there are also many reports that vitamin A deficiency is associated with non-responsiveness to antiviral treatment in HCV infected patients. So the present in silico study was aimed to find the relation between vitamin A deficiency and the NS5A protein's function in antiviral resistance...
2017: Acta Virologica
https://www.readbyqxmd.com/read/28510023/protein-rna-interactions-structural-biology-and-computational-modeling-techniques
#3
REVIEW
Susan Jones
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures...
December 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28505542/computational-modeling-of-protein-assemblies
#4
REVIEW
Neelesh Soni, M S Madhusudhan
Computational methods to predict the 3D structures of protein interactions fall into 3 categories-template based modeling, protein-protein docking and hybrid/integrative modeling. The two most important considerations for modeling methods are sampling and scoring conformations. Sampling has benefitted from techniques such as fast Fourier transforms (FFT), spherical harmonics and higher order manifolds. Scoring complexes to determine binding free energy is still a challenging problem. Rapid advances have been made in hybrid modeling where experimental data are amalgamated with computations...
May 12, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28500295/angiotensin-ii-type-1-adenosine-a-2a-receptor-oligomers-a-novel-target-for-tardive-dyskinesia
#5
Paulo A de Oliveira, James A R Dalton, Marc López-Cano, Adrià Ricarte, Xavier Morató, Filipe C Matheus, Andréia S Cunha, Christa E Müller, Reinaldo N Takahashi, Víctor Fernández-Dueñas, Jesús Giraldo, Rui D Prediger, Francisco Ciruela
Tardive dyskinesia (TD) is a serious motor side effect that may appear after long-term treatment with neuroleptics and mostly mediated by dopamine D2 receptors (D2Rs). Striatal D2R functioning may be finely regulated by either adenosine A2A receptor (A2AR) or angiotensin receptor type 1 (AT1R) through putative receptor heteromers. Here, we examined whether A2AR and AT1R may oligomerize in the striatum to synergistically modulate dopaminergic transmission. First, by using bioluminescence resonance energy transfer, we demonstrated a physical AT1R-A2AR interaction in cultured cells...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28499419/across-proteome-modeling-of-dimer-structures-for-the-bottom-up-assembly-of-protein-protein-interaction-networks
#6
Surabhi Maheshwari, Michal Brylinski
BACKGROUND: Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide interaction space at molecular level. Although a growing body of research shows that protein docking can, in principle, be used to predict biologically relevant interactions, the accuracy of the across-proteome identification of interacting partners and the selection of near-native complex structures still need to be improved...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28486912/structural-investigation-of-vinca-domain-tubulin-binders-by-pharmacophore-atom-based-qsar-docking-and-molecular-dynamics-simulations
#7
Mohd Athar, Mohsin Yousuf Lone, Vijay M Khedkar, Ashish Radadiya, Anamik Shah, Prakash C Jha
Vinca domain of tubulin protein is a potent binding domain for various microtubule targeting drugs (MTD). However, binding mechanism and structure-activity-relationship (SAR) of this domain is not well understood in terms of ligand-receptor interactions and structure functionality requirements. Possibly, this limits the exploitation of this domain for developing novel clinical leads. Therefore, any step towards modelling and comprehension is of central contour. With this objective, we present here an In-silico insight through the development of a robust pharmacophore model and SAR analysis on a set of 26 well known Vinca domain binders of tubulin protein...
May 9, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28483642/structural-insights-into-the-molecular-function-of-human-2fe-2s-bola1-grx5-and-2fe-2s-bola3-grx5-complexes
#8
Veronica Nasta, Andrea Giachetti, Simone Ciofi-Baffoni, Lucia Banci
Members of the monothiol glutaredoxin family and members of the BolA-like protein family have recently emerged as specific interacting partners involved in iron-sulfur protein maturation and redox regulation pathways. It is known that human mitochondrial BOLA1 and BOLA3 form [2Fe-2S] cluster-bridged dimeric heterocomplexes with the monothiol glutaredoxin GRX5. The structure and cluster coordination of the two [2Fe-2S] heterocomplexes as well as their molecular function are, however, not defined yet. Experimentally-driven structural models of the two [2Fe-2S] cluster-bridged dimeric heterocomplexes, the relative stability of the two complexes and the redox properties of the [2Fe-2S] cluster bound to these complexes are here presented on the basis of UV/vis, CD, EPR and NMR spectroscopy and computational protein-protein docking...
May 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28467969/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#9
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28460116/the-pepattract-web-server-for-blind-large-scale-peptide-protein-docking
#10
Sjoerd J de Vries, Julien Rey, Christina E M Schindler, Martin Zacharias, Pierre Tuffery
Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430871/cluspro-peptidock-efficient-global-docking-of-peptide-recognition-motifs-using-fft
#11
Kathryn A Porter, Bing Xia, Dmitri Beglov, Tanggis Bohnuud, Nawsad Alam, Ora Schueler-Furman, Dima Kozakov
Summary: We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide's final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28424069/ankplex-algorithmic-structure-for-refinement-of-near-native-ankyrin-protein-docking
#12
Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee, Chatchai Tayapiwatana
BACKGROUND: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet...
April 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28415766/anti-proliferative-role-of-recombinant-lethal-toxin-of-bacillus-anthracis-on-primary-mammary-ductal-carcinoma-cells-revealing-its-therapeutic-potential
#13
Rekha Khandia, Bramhadev Pattnaik, Katherukamem Rajukumar, Atul Pateriya, Sandeep Bhatia, Harshad Murugkar, Anil Prakash, Hare Krishna Pradhan, Kuldeep Dhama, Ashok Munjal, Sunil K Joshi
Bacillus anthracis secretes three secretary proteins; lethal factor (LF), protective antigen (PA) and edema factor (EF). The LF has ability to check proliferation of mammary tumors, chiefly depending on mitogen activated protein kinase (MAPK) signaling pathway. Evaluation of therapeutic potential of recombinant LF (rLF), recombinant PA (rPA) and lethal toxin (rLF + rPA = LeTx) on the primary mammary ductal carcinoma cells revealed significant (p < 0.01) reduction in proliferation of tumor cells with mean inhibition indices of 28...
March 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28413985/salvianolic-acid-b-decreases-the-generation-of-amyloid-%C3%AE-by-modulating-bace1-activity
#14
Siva Sundara Kumar Durairajan, Venkat Reddy Chirasani, Sravan Gopalakrishnan Shetty, Ashok Iyaswamy, Sandeep Malampati, Juxian Song, Liangfeng Liu, Jiandong Huang, Sanjib Senapati, Min Li
Generation and accumulation of the amyloid-β (Aβ) peptide after proteolytic processing of the full length amyloid precursor protein (FL-APP) by β-secretase (β-site APP cleaving enzyme or BACE1) and β -secretase is a main causal factor of Alzheimer's disease (AD). Thus, inhibition of BACE1, a rate-limiting enzyme in the production of Aβ, is an attractive therapeutic approach for the treatment of AD. Recent studies suggest that salvianolic acid B (Sal B) isolated from the radix of Salvia miltiorrhiza Bunge, a Chinese herbal medicine commonly used for the treatment of cardiovascular, cerebrovascular and liver diseases in China...
April 17, 2017: Current Alzheimer Research
https://www.readbyqxmd.com/read/28413973/docking-related-survey-on-natural-product-based-new-monoamine-oxidase-inhibitors-and-their-therapeutic-potential
#15
Priyanka Dhiman, Neelam Malik, Anurag Khatkar
This is an exciting period for research on monoamine oxidase and its effects on central nervous system. As the current hitting-one-target therapeutic strategy has become quite inefficient for the treatment of various neurological disorders. The objective of this review is to identify and critically discuss the computational development of multi-target natural and related ligand-MAO protein docking approaches in the study of monoamine oxidase (MAO) enzymes. Computational development of the new compounds form natural and related synthetic origin, active as MAO inhibitors (MAOIs) were discussed in some detail...
April 14, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28405240/targeting-the-ubiquitin-conjugating-enzyme-e2d4-for-cancer-drug-discovery-a-structure-based-approach
#16
Vishwanath Ramatenki, Ramakrishna Dumpati, Rajender Vadija, Santhiprada Vellanki, Sarita Rajender Potlapally, Rohini Rondla, Uma Vuruputuri
Cancer progression is a global burden. The incidence and mortality now reach 30 million deaths per year. Several pathways of cancer are under investigation for the discovery of effective therapeutics. The present study highlights the structural details of the ubiquitin protein 'Ubiquitin-conjugating enzyme E2D4' (UBE2D4) for the novel lead structure identification in cancer drug discovery process. The evaluation of 3D structure of UBE2D4 was carried out using homology modelling techniques. The optimized structure was validated by standard computational protocols...
April 2017: Journal of Chemical Biology
https://www.readbyqxmd.com/read/28370480/pop1-might-be-recruiting-its-type-ia-interface-for-nlrp3-mediated-pyd-pyd-interaction-insights-from-md-simulation
#17
Jitendra Maharana, Ashutosh Vats, Santwana Gautam, Bibhu Prasad Nayak, Sushil Kumar, Jasobanta Sendha, Sachinandan De
Inflammasomes are multiprotein caspase-activating complexes that enhance the maturation and release of proinflammatory cytokines (IL-1β and IL-18) in response to the invading pathogen and/or host-derived cellular stress. These are assembled by the sensory proteins (viz NLRC4, NLRP1, NLRP3, and AIM-2), adaptor protein (ASC), and effector molecule procaspase-1. In NLRP3-mediated inflammasome activation, ASC acts as a mediator between NLRP3 and procaspase-1 for the transmission of signals. A series of homotypic protein-protein interactions (NLRP3(PYD) :ASC(PYD) and ASC(CARD) :CASP1(CARD) ) propagates the downstream signaling for the production of proinflammatory cytokines...
April 3, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28356893/alzheimer-s-toxic-amyloid-beta-oligomers-unwelcome-visitors-to-the-na-k-atpase-alpha3-docking-station
#18
Thomas DiChiara, Nadia DiNunno, Jeffrey Clark, Riana Lo Bu, Erika N Cline, Madeline G Rollins, Yuesong Gong, David L Brody, Stephen G Sligar, Pauline T Velasco, Kirsten L Viola, William L Klein
Toxic amyloid beta oligomers (AβOs) are known to accumulate in Alzheimer's disease (AD) and in animal models of AD. Their structure is heterogeneous, and they are found in both intracellular and extracellular milieu. When given to CNS cultures or injected ICV into non-human primates and other non-transgenic animals, AβOs have been found to cause impaired synaptic plasticity, loss of memory function, tau hyperphosphorylation and tangle formation, synapse elimination, oxidative and ER stress, inflammatory microglial activation, and selective nerve cell death...
March 2017: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/28355486/molecular-recognition-in-mitochondrial-cytochromes-p450-that-catalyze-the-terminal-steps-of-corticosteroid-biosynthesis
#19
Hwei-Ming Peng, Richard J Auchus
The mitochondrial cytochromes P450 11B1 and P450 11B2 are responsible for the final stages of cortisol and aldosterone synthesis, respectively. Dysregulation of both enzymes has been implicated in secondary forms of hypertension. Molecular recognition of the cytochromes P450 with their corresponding redox partner is a key step in the catalytic cycle, yet the precise nature of the interaction of P450 11B1 or P450 11B2 with their proximal partner, adrenodoxin (Adx), is still unknown. Here, we obtained P450 11B1·Adx2 and P450 11B2·Adx2 complexes using the zero-length cross-linker ethyl-3-[3-(dimethylamino)propyl]carbodiimide, which formed best under low-ionic strength conditions...
April 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28346800/using-chemoinformatics-bioinformatics-and-bioassay-to-predict-and-explain-the-antibacterial-activity-of-nonantibiotic-food-and-drug-administration-drugs
#20
Nour Aldin Kahlous, Muhammad Al Mohdi Bawarish, Muhammad Arabi Sarhan, Manfred Küpper, Ali Hasaba, Mazen Rajab
Discovering of new and effective antibiotics is a major issue facing scientists today. Luckily, the development of computer science offers new methods to overcome this issue. In this study, a set of computer software was used to predict the antibacterial activity of nonantibiotic Food and Drug Administration (FDA)-approved drugs, and to explain their action by possible binding to well-known bacterial protein targets, along with testing their antibacterial activity against Gram-positive and Gram-negative bacteria...
April 2017: Assay and Drug Development Technologies
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