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https://www.readbyqxmd.com/read/28922141/towards-an-in-plane-methodology-to-track-breast-lesions-by-using-mammograms-and-patient-specific-finite-element-simulations
#1
Andres Lapuebla-Ferri, Jose Cegoñino-Banzo, Antonio-Jose Jimenez-Mocholi, Amaya Perez Del Palomar
In breast cancer screening or diagnosis, it is usual to combine different images in order to locate a lesion as accurately as possible. These images are generated by using a single or several imaging techniques. As X-ray based mammography is used widespread, a breast lesion is located in the same plane of the image (mammogram), but tracking of a breast lesion across mammograms corresponding to different views is a daring task for medical physicians. According to this, simulation tools and methodologies that use patient-specific numerical models can facilitate the task of fusing information from different images...
September 18, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28921985/computer-aided-identification-and-lead-optimization-of-dual-murine-double-minute-2-and-4-binders-structure-activity-relationship-studies-and-pharmacological-activity
#2
Mariateresa Giustiniano, Simona Daniele, Sveva Pelliccia, Valeria La Pietra, Deborah Pietrobono, Diego Brancaccio, Sandro Cosconati, Anna Messere, Stefano Giuntini, Linda Cerofolini, Marco Fragai, Claudio Luchinat, Sabrina Taliani, Giuseppe La Regina, Federico Da Settimo, Romano Silvestri, Claudia Martini, Ettore Novellino, Luciana Marinelli
The function of p53 protein, also known as "genome guardian", might be impaired by the over-expression of its primary cellular inhibitor, the murine double minute 2 protein (MDM2). However, the recent finding that MDM2-selective inhibitors induce high levels of its homolog MDM4, prompt us to identify, through a receptor-based virtual screening on an in house dababase, dual MDM2/MDM4 binders. Compound 1 turned out to possess an IC50 of 93.7 nM and of 4.6 nM on MDM2 and MDM4 respectively. A series of compounds were synthetized to optimize its activity on MDM2...
September 18, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28921842/anchorquery-rapid-online-virtual-screening-for-small-molecule-protein-protein-interaction-inhibitors
#3
David R Koes, Alexander Dömling, Carlos J Camacho
AnchorQuery ( http://anchorquery.csb.pitt.edu) is a web application for rational structure-based design of protein-protein interaction (PPI) inhibitors. A specialized variant of pharmacophore search is used to rapidly screen libraries consisting of more than 31 million synthesizable compounds biased by design to preferentially target PPIs. Every library compound is accessible through one-step multi-component reaction (MCR) chemistry and contains an anchor motif that is bioisosteric to an amino acid residue...
September 16, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28921079/identification-of-a-new-isoindole-2-yl-scaffold-as-a-qo-and-qi-dual-inhibitor-of-cytochrome-bc-1-complex-virtual-screening-synthesis-and-biochemical-assay
#4
Homa Azizian, Kowsar Bagherzadeh, Sophia Shahbazi, Niusha Sharifi, Massoud Amanlou
Respiratory chain ubiquinol-cytochrome (cyt) c oxidoreductase (cyt bc 1 or complex III) has been demonstrated as a promising target for numerous antibiotics and fungicide applications. In this study, a virtual screening of NCI diversity database was carried out in order to find novel Qo/Qi cyt bc 1 complex inhibitors. Structure-based virtual screening and molecular docking methodology were employed to further screen compounds with inhibition activity against cyt bc 1 complex after extensive reliability validation protocol with cross-docking method and identification of the best score functions...
September 18, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28918599/optimal-affinity-ranking-for-automated-virtual-screening-validated-in-prospective-d3r-grand-challenges
#5
Bentley M Wingert, Rick Oerlemans, Carlos J Camacho
The goal of virtual screening is to generate a substantially reduced and enriched subset of compounds from a large virtual chemistry space. Critical in these efforts are methods to properly rank the binding affinity of compounds. Prospective evaluations of ranking strategies in the D3R grand challenges show that for targets with deep pockets the best correlations (Spearman ρ ~ 0.5) were obtained by our submissions that docked compounds to the holo-receptors with the most chemically similar ligand. On the other hand, for targets with open pockets using multiple receptor structures is not a good strategy...
September 16, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28918321/extending-donor-size-in-d-a-%C3%AF-a-organic-dye-for-dye-sensitized-solar-cells-anti-aggregation-and-improving-electron-injection
#6
Yuan-Chun Hu, Wei-Lu Ding, Xing-Liang Peng, Ze-Sheng Li
We have theoretically designed two D-A-π-A dyes 3 and 4 based on the efficient references 1 and 2 by introducing an extra electron donor unit (D2). Via calculating the electronic structures of isolated dyes, we obtain that dyes 3 and 4 possess stronger light-harvesting efficiency imparted by the fluorescence energy transfer of D2 part, maintain comparable lifetime of excited states, and shorten the electron injection time significantly with regard to 1 and 2. Meanwhile, dye 3 positively shifts the edge of virtual states of TiO2 in a larger extent compared to its counterparts...
September 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28918098/identifying-novel-factor-xiia-inhibitors-with-pca-ga-svm-developed-vhts-models
#7
Jonathan Jun Feng Chen, Donald P Visco
There currently is renewed interest in blood clotting Factor XII as a potential target for thrombosis inhibition. Historically untargeted, there is little drug information with which to start drug candidate searches. Typical high-throughput screening can identify potential drug candidates, but is inefficient. Virtual high-throughput screening can be used to raise efficiency by focusing experimental efforts on compounds predicted to be active and is applied here to identify new Factor XIIa inhibitors. We combine principal component analysis, genetic algorithm and support vector machine to create the models used in the virtual high-throughput screening...
September 1, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28917147/combined-in-silico-approaches-for-the-identification-of-novel-inhibitors-of-human-islet-amyloid-polypeptide-hiapp-fibrillation
#8
Palak Patel, Krupali Parmar, Vivek K Vyas, Dhaval Patel, Mili Das
Human islet amyloid polypeptide (hIAPP) is a natively unfolded polypeptide hormone of glucose metabolism, which is co-secreted with insulin by the β-cells of the pancreas. In patients with type 2 diabetes, IAPP forms amyloid fibrils because of diabetes-associated β-cells dysfunction and increasing fibrillation, in turn, lead to failure of secretory function of β-cells. This provides a target for the discovery of small organic molecules against protein aggregation diseases. However, the binding mechanism of these molecules with monomers, oligomers and fibrils to inhibit fibrillation is still an open question...
September 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28917015/metronome-lkm-an-open-source-virtual-keyboard-driver-to-measure-experiment-software-latencies
#9
Pablo Garaizar, Miguel A Vadillo
Experiment software is often used to measure reaction times gathered with keyboards or other input devices. In previous studies, the accuracy and precision of time stamps has been assessed through several means: (a) generating accurate square wave signals from an external device connected to the parallel port of the computer running the experiment software, (b) triggering the typematic repeat feature of some keyboards to get an evenly separated series of keypress events, or (c) using a solenoid handled by a microcontroller to press the input device (keyboard, mouse button, touch screen) that will be used in the experimental setup...
September 15, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28913661/discovery-of-non-peptidic-small-molecule-inhibitors-of-cyclophilin-d-as-neuroprotective-agents-in-a%C3%AE-induced-mitochondrial-dysfunction
#10
Insun Park, Ashwini M Londhe, Ji Woong Lim, Beoung-Geon Park, Seo Yun Jung, Jae Yeol Lee, Sang Min Lim, Kyoung Tai No, Jiyoun Lee, Ae Nim Pae
Cyclophilin D (CypD) is a mitochondria-specific cyclophilin that is known to play a pivotal role in the formation of the mitochondrial permeability transition pore (mPTP).The formation and opening of the mPTP disrupt mitochondrial homeostasis, cause mitochondrial dysfunction and eventually lead to cell death. Several recent studies have found that CypD promotes the formation of the mPTP upon binding to β amyloid (Aβ) peptides inside brain mitochondria, suggesting that neuronal CypD has a potential to be a promising therapeutic target for Alzheimer's disease (AD)...
September 14, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28910858/overview-of-methods-and-strategies-for-conducting-virtual-small-molecule-screening
#11
Xavier Fradera, Kerim Babaoglu
Virtual screening (VS) in the context of drug discovery is the use of computational methods to discover novel ligands with a desired biological activity from within a larger collection of molecules. These techniques have been in use for many years, there is a wide range of methodologies available, and many successful applications have been reported in the literature. VS is often used as an alternative or a complement to High-throughput screening (HTS) or other methods to identify ligands for target validation or medicinal chemistry projects...
September 14, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28910705/pharmacophore-modeling-virtual-screening-and-molecular-docking-of-atpase-inhibitors-of-hsp70
#12
K Sangeetha, R P Sasikala, K S Meena
Heat shock protein 70 is an effective anticancer target as it influences many signaling pathways. Hence the study investigated the important pharmacophore feature required for ATPase inhibitors of HSP70 by generating a ligand based pharmacophore model followed by virtual based screening and subsequent validation by molecular docking in Discovery studio V4.0. The most extrapolative pharmacophore model (hypotheses 8) consisted of four hydrogen bond acceptors. Further validation by external test set prediction identified 200 hits from Mini Maybridge, Drug Diverse, SCPDB compounds and Phytochemicals...
June 26, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28901664/pharmacophore-based-virtual-screening-molecular-docking-molecular-dynamics-simulation-and-biological-evaluation-for-the-discovery-of-novel-brd4-inhibitors
#13
Guoyi Yan, Manzhou Hou, Jiang Luo, Chunlan Pu, Xueyan Hou, Suke Lan, Rui Li
Bromodomain is a recognition module in the signal transduction of acetylated histone. BRD4, one of the bromodomain members, is emerging as an attractive therapeutic target for several types of cancer. Therefore, in this study an attempt has been made to screen compounds from an integrated database containing 5.5 million compounds for BRD4 inhibitors by using pharmacophore based virtual screening, molecular docking, and molecular dynamics simulations. As a result, two molecules out of twelve hits were found to be active in bioactivity tests...
September 13, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28899791/toward-a-hierarchical-virtual-screening-and-toxicity-risk-analysis-for-identifying-novel-ca-xii-inhibitors
#14
Elmira Nazarshodeh, Sajjad Gharaghani
Carbonic anhydrase isoform XII (CA XII) is a potential target for cancer treatment. In this study, pharmacophore modeling, hierarchical virtual screening, and toxicity risk analysis were performed for identifying novel CA XII inhibitors. A pharmacophore model of two classes of CA XII inhibitors was generated. The pharmacophore model indicated the important features of inhibitors for the binding with the CA XII. The model was then utilized to screen the ZINC and CoCoCo databases for retrieving potential hit compounds of CA XII...
September 9, 2017: Bio Systems
https://www.readbyqxmd.com/read/28894629/isolation-characterization-and-in-silico-docking-studies-of-synergistic-estrogen-receptor-a-anticancer-polyphenols-from-syzygium-alternifolium-wt-walp
#15
Pulicherla Yugandhar, Konidala Kranthi Kumar, Pabbaraju Neeraja, Nataru Savithramma
AIM: This study aims to isolate, characterize, and in silico evaluate of anticancer polyphenols from different parts of Syzygium alternifolium. MATERIALS AND METHODS: The polyphenols were isolated by standard protocol and characterized using Fourier-transform infrared (FT-IR), High performance liquid chromatography - Photodiode array detector coupled with Electrospray ionization - mass spectrometry (MS/MS). The compounds were elucidated based on retention time and molecular ions (m/z) either by [M+H](+)/[M-H](-) with the comparison of standard phenols as well as ReSpect software tool...
July 2017: Journal of Intercultural Ethnopharmacology
https://www.readbyqxmd.com/read/28893570/phytoestrogenic-effect-of-inula-racemosa-hook-f-a-cardioprotective-root-drug-in-traditional-medicine
#16
Kalachaveedu Mangathayaru, Divya Raghavan, Srivani Telapolu, Sarah Kuruvilla, Kedike Balakrishna
ETHNOPHARMACOLOGICAL RELEVANCE: Roots of Inula racemosa are used as a cardio protective in Ayurveda in India, being prescribed as a medicine for precordial chest pain, cough and dyspnoea, both singly and as a poly herbal. AIM: Evaluation of Phytoestrogenic activity of the root extracts of Inula racemosa and compounds isolated therefrom in vivo, in silico and in vitro. MATERIALS AND METHODS: Alcohol (IrA) and hexane (IrH) extracts characterized by HPTLC/GC-MS analysis respectively and processed for compound isolation were evaluated for estrogenic activity (100 &250mg/kg bw) by the Immature rat uterotrophic assay using ethinylestradiol (EE -30µg/kg bw) as standard drug...
September 8, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28892749/virtual-screening-of-b-raf-kinase-inhibitors-a-combination-of-pharmacophore-modelling-molecular-docking-3d-qsar-model-and-binding-free-energy-calculation-studies
#17
Wen Zhang, Kai-Xiong Qiu, Fang Yu, Xiao-Guang Xie, Shu-Qun Zhang, Ya-Juan Chen, Hui-Ding Xie
B-Raf kinase has been identified as an important target in recent cancer treatment. In order to discover structurally diverse and novel B-Raf inhibitors (BRIs), a virtual screening of BRIs against ZINC database was performed by using a combination of pharmacophore modelling, molecular docking, 3D-QSAR model and binding free energy (ΔGbind) calculation studies in this work. After the virtual screening, six promising hit compounds were obtained, which were then tested for inhibitory activities of A375 cell lines...
August 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28892390/virtual-orbital-many-body-expansions-a-possible-route-towards-the-full-configuration-interaction-limit
#18
Janus J Eriksen, Filippo Lipparini, Jürgen Gauss
It is demonstrated how full configuration interaction (FCI) results in extended basis sets may be obtained to within sub-kJ/mol accuracy by decomposing the energy in terms of many-body expansions in the virtual orbitals of the molecular system at hand. This extension of the FCI application range lends itself to two unique features of the current approach, namely, that the total energy calculation can be performed entirely within considerably reduced orbital subspaces and may be so by means of embarrassingly parallel programming...
September 13, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28889312/discovering-selective-diguanylate-cyclase-inhibitors-from-pled-to-discrimination-of-the-active-site-of-cyclic-di-gmp-phosphodiesterases
#19
S Rinaldo, G Giardina, F Mantoni, A Paiardini, Alessio Paone, Francesca Cutruzzolà
One of the most important signals involved in controlling biofilm formation is represented by the intracellular second messenger 3',5'-cyclic diguanylic acid (c-di-GMP). Since the pathways involved in c-di-GMP biosynthesis and breakdown are found only in bacteria, targeting c-di-GMP metabolism represents an attractive strategy for the development of biofilm-disrupting drugs. Here, we present the workflow required to perform a structure-based design of inhibitors of diguanylate cyclases, the enzymes responsible for c-di-GMP biosynthesis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889160/interprofessional-education-in-allied-health-using-virtual-technologies
#20
Amber D Donnelly, Maheswari S Mukherjee, Jana Koth, Lisa Bartenhagen
BACKGROUND: Interprofessional education (IPE) is becoming increasingly prevalent in health science education, with the goal of preparing students to work collaboratively in teams within the healthcare environment. Students in our cytotechnology and radiation therapy (RT) programs used virtual technologies to demonstrate their professions using case studies. The purpose of this activity was to see if our students' knowledge of each other's professions and educational technologies increased and if the students had a better understanding of how they would work together in a healthcare team...
2017: Journal of Allied Health
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