NDLI: Efficient SDH computation in molecular simulations data

Please wait, while we are loading the content...

Serum antibody repertoire profiling using virtual antigen screen

Genome scale inference of transcriptional regulatory networks using mutual information on complex interactions

An iterative MapReduce approach to frequent subgraph mining in biological datasets

Feature extraction in protein sequences classification: a new stability measure

STEROID: in silico heuristic target combination identification for disease-related signaling networks

miHA-match: computational detection of tissue-specific minor histocompatibility antigens

Unraveling multiple miRNA-mRNA associations through a graph-based approach

High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems

Robustness measure for an adeno-associated viral shell self-assembly is accurately predicted by configuration space atlasing using EASAL

ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet

Decoding dendritic cell function through module and network analysis

A collective NMF method for detecting protein functional module from multiple data sources

Parallelization of the spectral deconvolution stage of the proteomic discovery process

A Monte Carlo approach to measure the robustness of Boolean networks

NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots

Using quantitative dose-response data to benchmark B-cell epitope prediction for antipeptide antibodies

A system for acquiring and management of ECG signals by using mobile devices: a support for first intervention in heart attacks

Improved multiple sequence alignments using coupled pattern mining

Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations

ArtSurf: a method for deformable partial matching of protein small-molecule binding sites

A multi-directional rapidly exploring random graph (mRRG) for protein folding

Supervised logistic principal component analysis for pathway based genome-wide association studies

Multi-target protein-chemical interaction prediction using task-regularized and boosted multi-task learning

Reverse engineering molecular hypergraphs

Functional site prediction by exploiting correlations between labels of interacting residues

Non-overlapping clone pooling for high-throughput sequencing

Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data

OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elements

Inferring ancestry in admixed populations using microarray probe intensities

Anaphora resolution in biomedical literature: a hybrid approach

Functional module identification by block modeling using simulated annealing with path relinking

Biased decoy sampling to aid the selection of near-native protein conformations

Protein blocks versus hydrogen bonds based alphabets for protein structure classification

Discovering geometric patterns in genomic data

Exploring objective functions and cross-terms in the optimization of an energy function for protein design

Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples

Automatic segmentation and quantification of filamentous structures in electron tomography

PseudoDomain: identification of processed pseudogenes based on protein domain classification

Complexity reduction of stochastic master equation simulation based on Kronecker product analysis

Algorithms for detecting complementary SNPs within a region of interest that are associated with diseases

Protein function prediction using weak-label learning

Detecting ECG abnormalities via transductive transfer learning

Biological interpretation of morphological patterns in histopathological whole-slide images

Predicting expression-related features of chromosomal domain organization with network-structured analysis of gene expression and chromosomal location

Multivariate hypergeometric similarity measure

A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure

Evolutionary analysis of functional modules in dynamic PPI networks

Alignment of real-time live-cell growth data for quantitative analysis of growth at the shoot apex of Arabidopsis thaliana: deducing the relationship between primordia growth, gene expression and cell behaviors

Parallel syntenic alignment on GPUs

Finding informative genes for prostate cancer: a general framework of integrating heterogeneous sources

A new algorithm for finding enriched regions in ChIP-Seq data

Hybrid pattern matching for complex ontology term recognition

Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse

Efficient implementation of the hybrid method for stochastic simulation of biochemical systems

A collective ranking method for genome-wide association studies

Parallel verlet neighbor list algorithm for GPU-optimized MD simulations

DACIDR: deterministic annealed clustering with interpolative dimension reduction using a large collection of 16S rRNA sequences

Signed network propagation for detecting differential gene expressions and DNA copy number variations

Memory-based local search for simplified protein structure prediction

Remote homology detection on alpha-structural proteins using simulated evolution

3D bone microarchitecture modeling and fracture risk prediction

An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads

Scalable genome scaffolding using integer linear programming

Alignment seeding strategies using contiguous pyrimidine purine matches

An integrated optimization framework for inferring two generation kinships and parental genotypes from microsatellite samples

Semantic querying over knowledge in biomedical text corpora annotated with multiple ontologies

Towards biophysical validation of constraint modeling for rigidity analysis of proteins

A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein

Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data

Predicting protective bacterial antigens using random forest classifiers

ADANET: inferring gene regulatory networks using ensemble classifiers

On enumerating the DNA sequences

Microarray vs. RNA-Seq: a comparison for active subnetwork discovery

Simulation and analysis of antibody aggregation on cell surfaces using motion planning and graph analysis

Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model

QSEA for fuzzy subgraph querying of KEGG pathways

Rational design of orthogonal libraries of protein coding genes

Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions

A pattern mining based integrative framework for biomarker discovery

A novel approach for mining representative spatial motifs of proteins

Systems biology approach to identify markers of differentiation in bladder cancer

454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crust

An in-depth analysis of the molecular dynamics and structural aspects of IKB proteins

mHMM (multivariate hidden Markov model) application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal polymerase-II (Pol II) pausing release

Phylogenetic and functional divergence analysis of vertebrate IRAK family members

Multi-level structural domain-domain interactions for prediction of obligate and non-obligate protein-protein interactions

Identification of protein stability patches that pinpoint key structural or functional sites

Searching for the relics of primitive codons

Efficient SDH computation in molecular simulations data

A computational metabolic model of the NG108-15 cell for high content drug screening with electrophysiological readout

A novel mathematical basis for predicting somatic single nucleotide variants from next-generation sequencing

Nuclear localization signal prediction based on sequential pattern mining

Pattern analysis: a web-based tool for analyzing response patterns in low-replication, many-treatment gene expression data

ngALL database: a flexible framework for the management and integration of childhood leukemia next generation sequencing data

Secondary structure predictions for long RNA sequences based on inversion excursions: preliminary results

Rapid efficient macromolecular substructure searching in a cloud

Classification of multicolor fluorescence in-situ hybridization (M-FISH) image using regularized multinomial logistic regression

Copy number variation estimation from multiple next-generation sequencing samples

Entropy-based evaluation function for the investigation of genetic code adaptability

Shortest paths ranking methodology to identify alterations in PPI networks of complex diseases

Prediction of candidate genes for neuropsychiatric disorders using feature-based enrichment

A graph-based cluster ensemble method to detect protein functional modules from multiple information sources

Macromolecular modeling of protein structure - SCI1 of Nicotiana tabacum L

A continuum hard-sphere model of protein adsorption

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data

Predicting possible directed-graph patterns of gene expressions in studies involving multiple treatments

A brief comparison of DSP and HMM methods for gene finding

Computational tool for large-scale GPIomic analysis

A machine-learning approach to retrieving diabetic retinopathy images

An evolutionary search framework to efficiently sample local minima in the protein conformational space

Empirical metabolite identification via GA feature selection and Bayes classification

A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources

gLIMS: Google cloud-based laboratory information management system for NMR metabolomics

A comparative study of codon adaptation in ssDNA and dsDNA phages

RNA-DV: an interactive tool for editing and visualizing RNA secondary structures

Robust differential co-expression discovery: an insight into pharmacodynamics of tyrosine kinase inhibitor

Towards sequence-based DNA flexibility analysis

Simulation and study of large-scale bacteria-materials interactions via BioScape enabled by GPUs

How to select microscopy image similarity metrics?

Approximate subspace pattern mining for mapping copy-number variations

Microbial source tracking by molecular fingerprinting

Random-walk: a stagnation recovery technique for simplified protein structure prediction

Efficient SDH computation in molecular simulations data

Content Provider	ACM Digital Library
Author	Pandit, Sagar Tu, Yi-Cheng Grupcev, Vladimir Chen, Shaoping Kumar, Anand
Abstract	Analysis of large particle or molecular simulation data is integral part of the basic-science research community. It often involves computing functions such as point-to-point interactions of particles. Spatial distance histogram (SDH) is one such vital computation in scientific discovery. SDH is frequently used to compute Radial Distribution Function (RDF), and it takes quadratic time to compute using naive approach. Naive SDH computation is even more expensive as it is computed continuously over certain period of time to analyze simulation systems. In this paper we look at different tree-based SDH computation techniques and briefly discuss about their performance. We present different strategies to improve the performance of these techniques. Specifically, we study the density map (DM) based SDH computation techniques. A DM is essentially a grid dividing simulated space into cells (3D cubes) of equal size (volume), which can be easily implemented by augmenting a Quad-tree (or Oct-tree) index. DMs are used in various configurations to compute SDH continuously over snapshots of the simulation system. The performance improvements using some of these configurations is presented in this paper. We also discuss the effect of utilizing computation power of Graphics Processing Units (GPUs) in computing SDH.
Starting Page	527
Ending Page	529
Page Count	3
File Format	PDF
ISBN	9781450316705
DOI	10.1145/2382936.2383010
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-10-07
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Molecular simulation Radial distribution function Protein structure Structural biology Spatial distance histogram
Content Type	Text
Resource Type	Article

Central Library (ISO-9001:2015 Certified)
Indian Institute of Technology Kharagpur
Kharagpur, West Bengal, India | PIN - 721302

See location in the Map
03222 282435
Mail: support@ndl.gov.in

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in