Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A dynamic data structure for flexible molecular maintenance and informatics.

ABSTRACT: We present the 'Dynamic Packing Grid' (DPG), a neighborhood data structure for maintaining and manipulating flexible molecules and assemblies, for efficient computation of binding affinities in drug design or in molecular dynamics calculations.DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e. updates) of atoms or groups of atoms. DPG also supports constant time neighborhood queries from arbitrary points. Our results for maintenance of molecular surface and polarization energy computations using DPG exhibit marked improvement in time and space requirements.http://www.cs.utexas.edu/~bajaj/cvc/software/DPG.shtml.

SUBMITTER: Bajaj C

PROVIDER: S-EPMC3008647 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A dynamic data structure for flexible molecular maintenance and informatics.

Bajaj Chandrajit C Chowdhury Rezaul Alam RA Rasheed Muhibur M

Bioinformatics (Oxford, England) 20101125 1

<h4>Motivation</h4>We present the 'Dynamic Packing Grid' (DPG), a neighborhood data structure for maintaining and manipulating flexible molecules and assemblies, for efficient computation of binding affinities in drug design or in molecular dynamics calculations.<h4>Results</h4>DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e. updates) of atoms or groups of atoms. DPG also supports constant time neig ...[more]

PMID: 21115440

Similar Datasets

Flexible informatics for linking experimental data to mathematical models via DataRail.

Project description:Linking experimental data to mathematical models in biology is impeded by the lack of suitable software to manage and transform data. Model calibration would be facilitated and models would increase in value were it possible to preserve links to training data along with a record of all normalization, scaling, and fusion routines used to assemble the training data from primary results.We describe the implementation of DataRail, an open source MATLAB-based toolbox that stores experimental data in flexible multi-dimensional arrays, transforms arrays so as to maximize information content, and then constructs models using internal or external tools. Data integrity is maintained via a containment hierarchy for arrays, imposition of a metadata standard based on a newly proposed MIDAS format, assignment of semantically typed universal identifiers, and implementation of a procedure for storing the history of all transformations with the array. We illustrate the utility of DataRail by processing a newly collected set of approximately 22 000 measurements of protein activities obtained from cytokine-stimulated primary and transformed human liver cells.DataRail is distributed under the GNU General Public License and available at http://code.google.com/p/sbpipeline/

| S-EPMC2617752 | biostudies-literature

Open data informatics and data repurposing for IBD.

Project description: Not available

| S-EPMC6687058 | biostudies-literature

Dynamic predictions using flexible joint models of longitudinal and time-to-event data.

Project description:Joint models for longitudinal and time-to-event data are particularly relevant to many clinical studies where longitudinal biomarkers could be highly associated with a time-to-event outcome. A cutting-edge research direction in this area is dynamic predictions of patient prognosis (e.g., survival probabilities) given all available biomarker information, recently boosted by the stratified/personalized medicine initiative. As these dynamic predictions are individualized, flexible models are desirable in order to appropriately characterize each individual longitudinal trajectory. In this paper, we propose a new joint model using individual-level penalized splines (P-splines) to flexibly characterize the coevolution of the longitudinal and time-to-event processes. An important feature of our approach is that dynamic predictions of the survival probabilities are straightforward as the posterior distribution of the random P-spline coefficients given the observed data is a multivariate skew-normal distribution. The proposed methods are illustrated with data from the HIV Epidemiology Research Study. Our simulation results demonstrate that our model has better dynamic prediction performance than other existing approaches. © 2017 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

| S-EPMC5381717 | biostudies-literature

Sdfconf: A Novel, Flexible, and Robust Molecular Data Management Tool.

Project description:Projects in chemo- and bioinformatics often consist of scattered data in various types and are difficult to access in a meaningful way for efficient data analysis. Data is usually too diverse to be even manipulated effectively. Sdfconf is data manipulation and analysis software to address this problem in a logical and robust manner. Other software commonly used for such tasks are either not designed with molecular and/or conformational data in mind or provide only a narrow set of tasks to be accomplished. Furthermore, many tools are only available within commercial software packages. Sdfconf is a flexible, robust, and free-of-charge tool for linking data from various sources for meaningful and efficient manipulation and analysis of molecule data sets. Sdfconf packages molecular structures and metadata into a complete ensemble, from which one can access both the whole data set and individual molecules and/or conformations. In this software note, we offer some practical examples of the utilization of sdfconf.

| S-EPMC8757437 | biostudies-literature

Inference of structure ensembles of flexible biomolecules from sparse, averaged data.

Project description:We present the theoretical foundations of a general principle to infer structure ensembles of flexible biomolecules from spatially and temporally averaged data obtained in biophysical experiments. The central idea is to compute the Kullback-Leibler optimal modification of a given prior distribution ?(x) with respect to the experimental data and its uncertainty. This principle generalizes the successful inferential structure determination method and recently proposed maximum entropy methods. Tractability of the protocol is demonstrated through the analysis of simulated nuclear magnetic resonance spectroscopy data of a small peptide.

| S-EPMC3820694 | biostudies-literature

Data Leakage and Loss in Biodiversity Informatics.

Project description:The field of biodiversity informatics is in a massive, "grow-out" phase of creating and enabling large-scale biodiversity data resources. Because perhaps 90% of existing biodiversity data nonetheless remains unavailable for science and policy applications, the question arises as to how these existing and available data records can be mobilized most efficiently and effectively. This situation led to our analysis of several large-scale biodiversity datasets regarding birds and plants, detecting information gaps and documenting data "leakage" or attrition, in terms of data on taxon, time, and place, in each data record. We documented significant data leakage in each data dimension in each dataset. That is, significant numbers of data records are lacking crucial information in terms of taxon, time, and/or place; information on place was consistently the least complete, such that geographic referencing presently represents the most significant factor in degradation of usability of information from biodiversity information resources. Although the full process of digital capture, quality control, and enrichment is important to developing a complete digital record of existing biodiversity information, payoffs in terms of immediate data usability will be greatest with attention paid to the georeferencing challenge.

| S-EPMC6235996 | biostudies-literature

Explainable and generalizable AI-driven multiscale informatics for dynamic system modelling.

Project description:Ultra-precision machining requires system modelling that both satisfies explainability and conforms to data fidelity. Existing modelling approaches, whether based on data-driven methods in present artificial intelligence (AI) or on first-principle knowledge, fall short of these qualities in high-demanding industrial applications. Therefore, this paper develops an explainable and generalizable 'grey-box' AI informatics method for real-world dynamic system modelling. Such a grey-box model serves as a multiscale 'world model' by integrating the first principles of the system in a white-box architecture with data-fitting black boxes for varying hyperparameters of the white box. The physical principles serve as an explainable global meta-structure of the real-world system driven by physical knowledge, while the black boxes enhance local fitting accuracy driven by training data. The grey-box model thus encapsulates implicit variables and relationships that a standalone white-box model or black-box model fails to capture. Case study on an industrial cleanroom high-precision temperature regulation system verifies that the grey-box method outperforms existing modelling methods and is suitable for varying operating conditions.

| S-EPMC11303764 | biostudies-literature

The Function Biomedical Informatics Research Network Data Repository.

Project description:The Function Biomedical Informatics Research Network (FBIRN) developed methods and tools for conducting multi-scanner functional magnetic resonance imaging (fMRI) studies. Method and tool development were based on two major goals: 1) to assess the major sources of variation in fMRI studies conducted across scanners, including instrumentation, acquisition protocols, challenge tasks, and analysis methods, and 2) to provide a distributed network infrastructure and an associated federated database to host and query large, multi-site, fMRI and clinical data sets. In the process of achieving these goals the FBIRN test bed generated several multi-scanner brain imaging data sets to be shared with the wider scientific community via the BIRN Data Repository (BDR). The FBIRN Phase 1 data set consists of a traveling subject study of 5 healthy subjects, each scanned on 10 different 1.5 to 4 T scanners. The FBIRN Phase 2 and Phase 3 data sets consist of subjects with schizophrenia or schizoaffective disorder along with healthy comparison subjects scanned at multiple sites. In this paper, we provide concise descriptions of FBIRN's multi-scanner brain imaging data sets and details about the BIRN Data Repository instance of the Human Imaging Database (HID) used to publicly share the data.

| S-EPMC4651841 | biostudies-literature

Dynamic contrast enhancement and flexible odor codes.

Project description:Sensory stimuli evoke spiking activities patterned across neurons and time that are hypothesized to encode information about their identity. Since the same stimulus can be encountered in a multitude of ways, how stable or flexible are these stimulus-evoked responses? Here we examine this issue in the locust olfactory system. In the antennal lobe, we find that both spatial and temporal features of odor-evoked responses vary in a stimulus-history dependent manner. The response variations are not random, but allow the antennal lobe circuit to enhance the uniqueness of the current stimulus. Nevertheless, information about the odorant identity is conf ounded due to this contrast enhancement computation. Notably, predictions from a linear logical classifier (OR-of-ANDs) that can decode information distributed in flexible subsets of neurons match results from behavioral experiments. In sum, our results suggest that a trade-off between stability and flexibility in sensory coding can be achieved using a simple computational logic.

| S-EPMC6076288 | biostudies-other

Towards Predictive Maintenance for Flexible Manufacturing Using FIWARE

Project description:Industry 4.0 has shifted the manufacturing related processes from conventional processes within one organization to collaborative processes across different organizations. For example, product design processes, manufacturing processes, and maintenance processes across different factories and enterprises. This complex and competitive collaboration requires the underlying system architecture and platform to be flexible and extensible to support the demands of dynamic collaborations as well as advanced functionalities such as big data analytics. Both operation and condition of the production equipment are critical to the whole manufacturing process. Failures of any machine tools can easily have impact on the subsequent value-added processes of the collaboration. Predictive maintenance provides a detailed examination of the detection, location and diagnosis of faults in related machineries using various analyses. In this context, this paper explores how the FIWARE framework supports predictive maintenance. Specifically, it looks at applying a data driven approach to the Long Short-Term Memory Network (LSTM) model for machine condition and remaining useful life to support predictive maintenance using FIWARE framework in a modular fashion.

| S-EPMC7225515 | 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