Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High Throughput Profiling of Molecular Shapes in Crystals.

ABSTRACT: Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design.

SUBMITTER: Spackman PR

PROVIDER: S-EPMC4764928 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Prospective, high-throughput molecular profiling of human gliomas.

Project description:Gliomas consist of multiple histologic and molecular subtypes with different clinical phenotypes and responsiveness to treatment. However, enrollment criteria for clinical trials still largely do not take into account these underlying molecular differences. We have incorporated a high-throughput tumor genotyping program based on the ABI SNaPshot platform as well as other molecular diagnostic tests into the standard evaluation of glioma patients in order to assess whether prospective molecular profiling would allow rational patient selection onto clinical trials. From 218 gliomas we prospectively collected SNaPshot genotyping data on 68 mutated loci from 15 key cancer genes along with data from clinical assays for gene amplification (EGFR, PDGFRA, MET), 1p/19q co-deletion and MGMT promoter methylation. SNaPshot mutations and focal gene amplifications were detected in 38.5 and 47.1 % of glioblastomas, respectively. Genetic alterations in EGFR, IDH1 and PIK3CA closely matched frequencies reported in recent studies. In addition, we identified events that are rare in gliomas although are known driver mutations in other cancer types, such as mutations of AKT1, BRAF and KRAS. Patients with genetic alterations that activate signaling pathways were enrolled onto genetically selective clinical trials for malignant glioma as well as for other solid cancers. High-throughput molecular profiling incorporated into the routine clinical evaluation of glioma patients may enable the rational selection of patients for targeted therapy clinical trials and thereby improve the likelihood that such trials succeed.

| S-EPMC3583376 | biostudies-literature

High-Throughput Acoustofluidic Self-Assembly of Colloidal Crystals.

Project description:Colloidal crystals are encountered in a variety of energy-harvesting applications, where they serve as waveguides or filters for electromagnetic and electro-optic energy. Techniques such as electric or magnetic assembly are used to assemble colloidal crystals, but are limited by crystal size, yield, and throughput. This article demonstrates the continuous, high-throughput assembly of two-dimensional (2D)-colloidal crystals in an acoustofluidic flow cell. The device is fabricated using off-the-shelf components and does not require a clean-room access. An experimental state diagram shows how the fluid flow rate and voltage applied to the piezoelectric element in our device can tune the crystal microstructure. Highly ordered colloidal crystals are continuously assembled in less than a minute with a throughput yield of several hundred particles per minute using this device. The acoustically assembled ordered 2D crystals are immobilized using a UV-curable resin and extracted as ordered polymer-particle fibers, demonstrating the ability of using acoustic fields to assemble ordered structures embedded in bulk materials. Particle tracking is used to construct the cross-channel particle distribution to understand the effect of acoustic compression on colloidal crystal assembly. Microparticle image velocimetry data is compared to a theoretical transport model to quantify the effect fluid flow and acoustic trapping has on the colloidal crystal ensemble.

| S-EPMC6641480 | biostudies-literature

High-Throughput Microfluidic Characterization of Erythrocyte Shapes and Mechanical Variability.

Project description:The motion of red blood cells (RBCs) in microchannels is important for microvascular blood flow and biomedical applications such as blood analysis in microfluidics. The current understanding of the complexity of RBC shapes and dynamics in microchannels is mainly based on several simulation studies, but there are a few systematic experimental investigations. Here, we present a combined study that systematically characterizes RBC behavior for a wide range of flow rates and channel sizes. Even though simulations and experiments generally show good agreement, experimental observations demonstrate that there is no single well-defined RBC state for fixed flow conditions but rather a broad distribution of states. This result can be attributed to the inherent variability in RBC mechanical properties, which is confirmed by a model that takes the variation in RBC shear elasticity into account. This represents a significant step toward a quantitative connection between RBC behavior in microfluidic devices and their mechanical properties, which is essential for a high-throughput characterization of diseased cells.

| S-EPMC6626834 | biostudies-literature

Estimation and prediction of ellipsoidal molecular shapes in organic crystals based on ellipsoid packing.

Project description:Crystal structure prediction has been one of the fundamental and challenging problems in materials science. It is computationally exhaustive to identify molecular conformations and arrangements in organic molecular crystals due to complexity in intra- and inter-molecular interactions. From a geometrical viewpoint, specific types of organic crystal structures can be characterized by ellipsoid packing. In particular, we focus on aromatic systems which are important for organic semiconductor materials. In this study, we aim to estimate the ellipsoidal molecular shapes of such crystals and predict them from single molecular descriptors. First, we identify the molecular crystals with molecular centroid arrangements that correspond to affine transformations of four basic cubic lattices, through topological analysis of the dataset of crystalline polycyclic aromatic molecules. The novelty of our method is that the topological data analysis is applied to arrangements of molecular centroids intead of those of atoms. For each of the identified crystals, we estimate the intracrystalline molecular shape based on the ellipsoid packing assumption. Then, we show that the ellipsoidal shape can be predicted from single molecular descriptors using a machine learning method. The results suggest that topological characterization of molecular arrangements is useful for structure prediction of organic semiconductor materials.

| S-EPMC7526905 | biostudies-literature

DNA origami single crystals with Wulff shapes.

Project description:DNA origami technology has proven to be an excellent tool for precisely manipulating molecules and colloidal elements in a three-dimensional manner. However, fabrication of single crystals with well-defined facets from highly programmable, complex DNA origami units is a great challenge. Here, we report the successful fabrication of DNA origami single crystals with Wulff shapes and high yield. By regulating the symmetries and binding modes of the DNA origami building blocks, the crystalline shapes can be designed and well-controlled. The single crystals are then used to induce precise growth of an ultrathin layer of silica on the edges, resulting in mechanically reinforced silica-DNA hybrid structures that preserve the details of the single crystals without distortion. The silica-infused microcrystals can be directly observed in the dry state, which allows meticulous analysis of the crystal facets and tomographic 3D reconstruction of the single crystals by high-resolution electron microscopy.

| S-EPMC8140131 | biostudies-literature

High-throughput microRNA profiling of pediatric high-grade gliomas.

Project description:BackgroundHigh-grade gliomas (HGGs) account for 15% of all pediatric brain tumors and are a leading cause of cancer-related mortality and morbidity. Pediatric HGGs (pHGGs) are histologically indistinguishable from their counterpart in adulthood. However, recent investigations indicate that differences occur at the molecular level, thus suggesting that the molecular path to gliomagenesis in childhood is distinct from that of adults. MicroRNAs (miRNAs) have been identified as key molecules in gene expression regulation, both in development and in cancer. miRNAs have been investigated in adult high-grade gliomas (aHGGs), but scant information is available for pHGGs.MethodsWe explored the differences in microRNAs between pHGG and aHGG, in both fresh-frozen and paraffin-embedded tissue, by high-throughput miRNA profiling. We also evaluated the biological effects of miR-17-92 cluster silencing on a pHGG cell line.ResultsComparison of miRNA expression patterns in formalin versus frozen specimens resulted in high correlation between both types of samples. The analysis of miRNA profiling revealed a specific microRNA pattern in pHGG with an overexpression and a proliferative role of the miR-17-92 cluster. Moreover, we highlighted a possible quenching function of miR-17-92 cluster on its target gene PTEN, together with an activation of tumorigenic signaling such as sonic hedgehog in pHGG.ConclusionsOur results suggest that microRNA profiling represents a tool to distinguishing pediatric from adult HGG and that miR-17-92 cluster sustains pHGG.

| S-EPMC3895388 | biostudies-literature

High-throughput protein profiling for detecting colorectal cancer protein expression and prognosis

Project description:Interventions: Gold Standard:1. physical examination - digital rectal examination; 2. laboratory examination - blood routine, fecal occult blood test; 3. imaging examination - X-ray angiography, ultrasound; 4. endoscopy - rectal sigmoidoscopy; 5. clinical outcomes The gold standard is histopathology.;Index test:Disease or healthy tissue specimen proteomics, peripheral blood, exosome protein and free DNA, urine and fecal metabolites. Primary outcome(s): Proteomics;SPF;Survival time Study Design: Sequential

| 2684555 | ecrin-mdr-crc

High-throughput screening of 2D van der Waals crystals with plastic deformability.

Project description:Inorganic semiconductors exhibit multifarious physical properties, but they are prevailingly brittle, impeding their application in flexible and hetero-shaped electronics. The exceptional plasticity discovered in InSe crystal indicates the existence of abundant plastically deformable two-dimensional van der Waals (2D vdW) materials, but the conventional trial-and-error method is too time-consuming and costly. Here we report on the discovery of tens of potential 2D chalcogenide crystals with plastic deformability using a nearly automated and efficient high-throughput screening methodology. Seven candidates e.g., famous MoS2, GaSe, and SnSe2 2D materials are carefully verified to show largely anisotropic plastic deformations, which are contributed by both interlayer and cross-layer slips involving continuous breaking and reconstruction of chemical interactions. The plasticity becomes a new facet of 2D materials for deformable or flexible electronics.

| S-EPMC9723169 | biostudies-literature

High-Throughput Preparation and High-Throughput Detection of Polymer-Dispersed Liquid Crystals Based on Ink-Jet Printing and Grayscale Value Analysis.

Project description:In this paper, based on high-throughput technology, polymer dispersed liquid crystals (PDLC) composed of pentaerythritol tetra (2-mercaptoacetic acid) (PETMP), trimethylolpropane triacrylate (TMPTA), and polyethylene glycol diacrylate (PEGD 600) were investigated in detail. A total of 125 PDLC samples with different ratios were quickly prepared using ink-jet printing. Based on the method of machine vision to identify the grayscale level of samples, as far as we know, it is the first time to realize high-throughput detection of the electro-optical performance of PDLC samples, which can quickly screen out the lowest saturation voltage of batch samples. Additionally, we compared the electro-optical test results of manual and high-throughput preparation PDLC samples and discovered that they had very similar electro-optical characteristics and morphologies. This demonstrated the viability of PDLC sample high-throughput preparation and detection, as well as promising application prospects, and significantly increased the efficiency of PDLC sample preparation and detection. The results of this study will contribute to the research and application of PDLC composites in the future.

| S-EPMC10005514 | biostudies-literature

Atomic stiffness for bulk modulus prediction and high-throughput screening of ultraincompressible crystals.

Project description:Determining bulk moduli is central to high-throughput screening of ultraincompressible materials. However, existing approaches are either too inaccurate or too expensive for general applications, or they are limited to narrow chemistries. Here we define a microscopic quantity to measure the atomic stiffness for each element in the periodic table. Based on this quantity, we derive an analytic formula for bulk modulus prediction. By analyzing numerous crystals from first-principles calculations, this formula shows superior accuracy, efficiency, universality, and interpretability compared to previous empirical/semiempirical formulae and machine learning models. Directed by our formula predictions and verified by first-principles calculations, 47 ultraincompressible crystals rivaling diamond are identified from over one million material candidates, which extends the family of known ultraincompressible crystals. Finally, treasure maps of possible elemental combinations for ultraincompressible crystals are created from our theory. This theory and insights provide guidelines for designing and discovering ultraincompressible crystals of the future.

| S-EPMC10352355 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data