NDLI: An Artificial Neural Network Based Approach for Identification of Native Protein Structures Using an Extended Forcefield

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2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2013 IEEE International Conference on Bioinformatics and Biomedicine

2012 IEEE International Conference on Bioinformatics and Biomedicine

2011 IEEE International Conference on Bioinformatics and Biomedicine

Table of Contents

Committee Lists

Program Committee Members

Inferring Functional Groups from Microbial Gene Catalogue with Probabilistic Topic Models

Stratified Random Forest for Genome-wide Association Study

Structure-based RNA Function Prediction Using Elastic Shape Analysis

VASP-S: A Volumetric Analysis and Statistical Model for Predicting Steric Influences on Protein-Ligand Binding Specificity

Fast Algorithm for Clustering a Large Number of Protein Structural Decoys

Active Protein Interaction Network and Its Application on Protein Complex Detection

Intrinsic Disorder in Putative Protein Sequences

Simplification Methods for Maximum Parsimony: A Relational View

Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome

A New Measurement for Evaluating Clusters in Protein Interaction Networks

Phylogenomic Analysis of the Phenylalanine Ammonia Lyase Gene Family in Loblolly Pine (Pinus Taeda L.)

Data-Driven Insights into Deletions of Mycobacterium tuberculosis Complex Chromosomal DR Region Using Spoligoforests

Efficient and Fast Analysis for Detecting High Order Gene-by-Gene Interactions in a Genome-Wide Association Study

Simultaneous Prediction of RNA Secondary Structure and Helix Coaxial Stacking

Clustering PPI Data Based on Bacteria Foraging Optimization Algorithm

imiRTP: An Integrated Method to Identifying miRNA-target Interactions in Arabidopsis thaliana

Emulating Insertion and Deletion Events in Genome Rearrangement Analysis

Benchmarking Short Sequence Mapping Tools

Populating Local Minima in the Protein Conformational Space

A Simple and Accurate Method for Rogue Taxon Identification

An Improved Graph Entropy-based Method for Identifying Protein Complexes

Discovering Drug-Protein Interactions Based on their Fingerprints

Approximate Common Intervals in Multiple Genome Comparison

Employing Weighted Biological Network Structure for Finding Disease Genetic Markers in SNP Association Studies

mrNA: The MPI Randomized Numerical Aligner

Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties

No-Reference Compression of Genomic Data Stored in FASTQ Format

Improved RNA-Seq Partitions in Linear Models for Isoform Quantification

Chronology-Sensitive Hierarchical Clustering of Pyrosequenced DNA Samples of E. coli: A Case Study

A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors

Stochastic Models for Studying the Degradation of mRNA Molecules

Generalized Adjacency in Genetic Networks and the Conservation of Functional Gene Clusters

Functional Gene Detection and Clustering from Seed Gene Sets

Predicing Yeast Synthetic Lethal Genetic Interactions Using Short Polypeptide Clusters

Improve Accuracy of Peptide Identification with Consistency between Peptides

Delay-Dependent Stability for Genetic Regulatory Networks

Reconstruction of Large-Scale Gene Regulatory Networks Using Bayesian Model Averaging

Inferring Transcript Phylogenies

Modeling Gene Regulatory Subnetworks from Time Course Gene Expression Data

Evolutionary Conservation of Human Phosphorylation Sites

Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures

Global Network Alignment Based on Multiple Hub Seeds

Employing Machine Learning Techniques for Data Enrichment: Increasing the Number of Samples for Effective Gene Expression Data Analysis

Semi-supervised Learning of Alternatively Spliced Exons Using Co-training

A Computational Pipeline for LC-MS/MS Based Metabolite Identification

Stability Analysis of Feature Ranking Techniques on Biological Datasets

Predicting Kinase-specific Phosphorylation Sites Using a Multitask Classification Framework

Bayesian Alignment Model for LC-MS Data

Biological Interpretation of Model-Reference Adaptive Control in a Mass Action Kinetics Metabolic Pathway Model

Microarray Time-Series Data Clustering Using Rough-Fuzzy C-Means Algorithm

Prediction and Evaluation of miRNA -- Target Gene Pairs Using K-means Clustering and Bipartite Graphs with Statistical Scoring

A Network Biology Approach to Predicting Drug Cardiotoxicity

Multi-label Learning for Protein Subcellular Location Prediction

Deconvolution of Microarray Data Predicts Transcriptionally Regulated Protein Kinases of Plasmodium falciparum

Systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data

Identifying Ovarian Cancer Chemotherapy Response Relevant Gene Cliques

Improved Quantification of Labeled LC-MS

Formal Modeling and Analysis of Biological Regulatory Networks Using SPIN

Learning Condition-Dependent Dynamical PPI Networks from Conflict-Sensitive Phosphorylation Dynamics

Cardinal Multiridgelet-based Prostate Cancer Histological Image Classification for Gleason Grading

A Differential Evolution-Based System Supporting Medical Diagnosis through Automatic Knowledge Extraction from Databases

A Posture Scheduling Algorithm Using Constrained Shortest Path to Prevent Pressure Ulcers

Computer-Based Image Analysis of Liver Steatosis with Large-Scale Microscopy Imagery and Correlation with Magnetic Resonance Imaging Lipid Analysis

Predicting Malignancy from Mammography Findings and Surgical Biopsies

PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design

Coupling Oriented Hidden Markov Random Field Model with Local Clustering for Segmenting Blood Vessels and Measuring Spatial Structures in Images of Tumor Microenvironment

A Pattern Mining Approach for Classifying Multivariate Temporal Data

3D Neuron Tip Detection in Volumetric Microscopy Images

Automatic Summarization of Results from Clinical Trials

Cell Resolution 3D Reconstruction of Developing Multilayer Tissues from Sparsely Sampled Volumetric Microscopy Images

Diagnostic Classification of Digital Mammograms by Wavelet-Based Spectral Tools: A Comparative Study

Cost-Sensitive Classification on Pathogen Species of Bacterial Meningitis by Surface Enhanced Raman Scattering

Classification of Schizophrenia Patients with Combined Analysis of SNP and fMRI Data Based on Sparse Representation

A Novel Algorithm for Multi-class Cancer Diagnosis on MALDI-TOF Mass Spectra

Identification of Breast Cancer Gene Signature in Protein Interaction Network Using Graph Centrality

Efficient Multiple Samples aCGH Analysis for Rare CNVs Detection

Motion Artifact Correction in ASL images: An Improved Automated Procedure

Object Segmentation by Comparison of Active Contour Snake and Level Set in Biomedical Applications

Preserving Narratives in Electronic Health Records

Histological Image Feature Mining Reveals Emergent Diagnostic Properties for Renal Cancer

A Framework for Personalized Medicine with Reverse Phase Protein Array and Drug Sensitivity

Mental Stress Detection Based on Soft Computing Techniques

Protein Structure Visualization by Dimension Reduction and Texture Mapping

Detecting Pathway Cross-Talks by Analyzing Conserved Functional Modules across Multiple Phenotype-Expressing Organisms

Probabilistic Signal Network Models from Multiple Replicates of Sparse Time-Course Data

Promoting Ranking Diversity for Biomedical Information Retrieval Based on LDA

ENteric Immunity SImulator: A Tool for in silico Study of Gut Immunopathologies

Essential Protein Discovery Based on Network Motif and Gene Ontology

Multi-class Joint Rule Extraction and Feature Selection for Biological Data

Improving Prediction Accuracy of Protein-DNA Docking with GPU Computing

Ontology Graph Based Query Expansion for Biomedical Information Retrieval

BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis

An Artificial Neural Network Based Approach for Identification of Native Protein Structures Using an Extended Forcefield

Finding Informative Genes from Multiple Microarray Experiments: A Graph-based Consensus Maximization Model

Semantic Predications for Complex Information Needs in Biomedical Literature

IDDI: The Integrated Domain-Domain Interaction Analysis System

Probabilistic Partial Least Square Regression: A Robust Model for Quantitative Analysis of Raman Spectroscopy Data

A Term Association Approach for Genomics Information Retrieval

Protein Sequence Classification Using Feature Hashing

Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering

ProKinO: A Framework for Protein Kinase Ontology

Toward a Cooperative Natural Language Query Interface for Biological Databases

Supervised Link Discovery on Large-Scale Biomedical Concept Networks

Assessment of Cluster Overlaps to Improve Accuracy of Module Detection from PPI Networks

Internal Evaluation Measures as Proxies for External Indices in Clustering Gene Expression Data

An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents

Identifying Protein Complexes from PPI Networks Using GO Semantic Similarity

Visually Relating Gene Expression and in vivo DNA Binding Data

Detection of Conflicts and Inconsistencies in Taxonomy-Based Authorization Policies

Bayesian Classifiers for Chemical Toxicity Prediction

Efficient Calculation of Structural Similarity Threshold for the SCAN Network Clustering Algorithm

Hypergeometric Similarity Measure for Spatial Analysis in Tissue Imaging Mass Spectrometry

Literature-based Evaluation of Microarray Normalization Procedures

RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure

R-PASS: A Fast Structure-Based RNA Sequence Alignment Algorithm

Using Rules to Investigate the Differences in Partonomy between Biomedical Ontologies

A Comparative Assessment of Conventional and Machine-Learning-Based Scoring Functions in Predicting Binding Affinities of Protein-Ligand Complexes

Wavelet and PCA for Metabolic Network Comparison

Mining Gene-centric Relationships from Literature to Support Drug Discovery

Hypothesis Generation and Evaluation in Clinical Trial Design

Mining Protein Interactions and Gene Expression Data to Gain Insights into Drug-induced Toxicity Mechanisms

Data Exploration in Secondary Use of Healthcare Data

Opening the Door to Electronic Medical Records: Using Informatics to Overcome Terabytes

Uniting Data for Memory: Building Informatics against Alzheimer's

Decision Support in Safety Intelligence Using Pharmaconnect Knowledgebase

Generating More Knowledge from Our Data and More Value from Our Studies: The Value of Expert Information Science Skills

2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2009 IEEE International Conference on Bioinformatics and Biomedicine

2008 IEEE International Conference on Bioinformatics and Biomedicine

2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)

An Artificial Neural Network Based Approach for Identification of Native Protein Structures Using an Extended Forcefield

Content Provider	IEEE Xplore Digital Library
Author	Fawcett, Timothy Matthew Irausquin, Stephanie Simin, Mikhail Valafar, Homayoun
Copyright Year	2011
Abstract	Current protein force fields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the force fields do not take into account the use of hydrogen bonds which are important for secondary structure creation and stabilization of proteins. SCOPE is an open-source program that generates proteins from rotamer space. It then creates a force field that uses only non-bonded and hydrogen bond energy terms to create a profile for a given protein. The profiles can then be used in an artificial neural network to create a linear model which is funneled to the true protein conformation.
Starting Page	500
Ending Page	505
File Size	403047
Page Count	6
File Format	PDF
ISBN	9781457717994
DOI	10.1109/BIBM.2011.53
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-11-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	artificial neural networks Conferences protein energetics protein conformation Bioinformatics hydrogen bonds
Content Type	Text
Resource Type	Article

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