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58 papers found.
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AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields

Motivation: Protein intrinsically disordered regions (IDRs) play an important role in many biological processes. Two key properties of IDRs are (i) the occurrence is proteome-wide and (ii) the ratio of disordered residues is about 6%, which makes it challenging to accurately predict IDRs. Most IDR prediction methods use sequence profile to improve accuracy, which prevents its...

RaptorX-Property: a web server for protein structure property prediction

RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in...

CoinFold: a web server for protein contact prediction and contact-assisted protein folding

CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the...

Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning

Motivation: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However, contact prediction is still challenging especially for proteins without a large number of sequence homologs. Results: This article...

Exploiting ontology graph for predicting sparsely annotated gene function

Motivation: Systematically predicting gene (or protein) function based on molecular interaction networks has become an important tool in refining and enhancing the existing annotation catalogs, such as the Gene Ontology (GO) database. However, functional labels with only a few (<10) annotated genes, which constitute about half of the GO terms in yeast, mouse and human, pose a...

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model...

Enhanced Photovoltage Response of Hematite-X-Ferrite Interfaces (X = Cr, Mn, Co, or Ni)

High-fluorescent p-X-ferrites (XFe2O4; XFO; X = Fe, Cr, Mn, Co, or Ni) embedded in n-hematite (Fe2O3) surfaces were successfully fabricated via a facile bio-approach using Shewanella oneidensis MR-1. The results revealed that the X ions with high/low work functions modify the unpaired spin Fe2+–O2− orbitals in the XFe2O4 lattices to become localized paired spin orbitals at the...

Local Plasticity of Dendritic Excitability Can Be Autonomous of Synaptic Plasticity and Regulated by Activity-Based Phosphorylation of Kv4.2

While plasticity is typically associated with persistent modifications of synaptic strengths, recent studies indicated that modulations of dendritic excitability may form the other part of the engram and dynamically affect computational processing and output of neuronal circuits. However it remains unknown whether modulation of dendritic excitability is controlled by synaptic...

The Frequency of Patient-Initiated Violence and Its Psychological Impact on Physicians in China: A Cross-Sectional Study

Introduction In China, the severity of medical disputes has greatly increased during the past two decades, which has caused various adverse outcomes for health professionals. Previous research on violence in healthcare settings has primarily examined the occurrence of patient-initiated violence and its effects on physicians, but few studies have focused on the impact of the...

Mechanism of Fluorescence Enhancement of Biosynthesized XFe2O4–BiFeO3 (X = Cr, Mn, Co, or Ni) Membranes

Ferrites–bismuth ferrite is an intriguing option for medical diagnostic imaging device due to its magnetoelectric and enhanced near-infrared fluorescent properties. However, the embedded XFO nanoparticles are randomly located on the BFO membranes, making implementation in devices difficult. To overcome this, we present a facile bio-approach to produce XFe2O4–BiFeO3 (XFO–BFO) (X...

Mechanism of Fluorescence Enhancement of Biosynthesized XFe2O4–BiFeO3 (X = Cr, Mn, Co, or Ni) Membranes

Ferrites–bismuth ferrite is an intriguing option for medical diagnostic imaging device due to its magnetoelectric and enhanced near-infrared fluorescent properties. However, the embedded XFO nanoparticles are randomly located on the BFO membranes, making implementation in devices difficult. To overcome this, we present a facile bio-approach to produce XFe2O4–BiFeO3 (XFO–BFO) (X...

Blood pressure and expression of microRNAs in whole blood

Background Blood pressure (BP) is a complex, multifactorial clinical outcome driven by genetic susceptibility, behavioral choices, and environmental factors. Many molecular mechanisms have been proposed for the pathophysiology of high BP even as its prevalence continues to grow worldwide, increasing morbidity and marking it as a major public health concern. To address this, we...

Discovering Link Communities in Complex Networks by an Integer Programming Model and a Genetic Algorithm

Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some...

Lynx: a knowledge base and an analytical workbench for integrative medicine

Lynx (http://lynx.ci.uchicago.edu) is a web-based database and a knowledge extraction engine. It supports annotation and analysis of high-throughput experimental data and generation of weighted hypotheses regarding genes and molecular mechanisms contributing to human phenotypes or conditions of interest. Since the last release, the Lynx knowledge base (LynxKB) has been...

A conditional neural fields model for protein threading

Motivation: Alignment errors are still the main bottleneck for current template-based protein modeling (TM) methods, including protein threading and homology modeling, especially when the sequence identity between two proteins under consideration is low (<30%). Results: We present a novel protein threading method, CNFpred, which achieves much more accurate sequence–template...

Elementary signaling modes predict the essentiality of signal transduction network components

Background Understanding how signals propagate through signaling pathways and networks is a central goal in systems biology. Quantitative dynamic models help to achieve this understanding, but are difficult to construct and validate because of the scarcity of known mechanistic details and kinetic parameters. Structural and qualitative analysis is emerging as a feasible and useful...

Two-stage flux balance analysis of metabolic networks for drug target identification

Background Efficient identification of drug targets is one of major challenges for drug discovery and drug development. Traditional approaches to drug target identification include literature search-based target prioritization and in vitro binding assays which are both time-consuming and labor intensive. Computational integration of different knowledge sources is a more effective...

Functional analysis of Flavonoid 3′,5′-hydroxylase from Tea plant (Camellia sinensis): critical role in the accumulation of catechins

Background Flavonoid 3′,5′-hydroxylase (F3′5′H), an important branch point enzyme in tea plant flavan-3-ol synthesis, belongs to the CYP75A subfamily and catalyzes the conversion of flavones, flavanones, dihydroflavonols and flavonols into 3′,4′,5′-hydroxylated derivatives. However, whether B-ring hydroxylation occurs at the level of flavanones and/or dihydroflavonols, in vivo...

Inferring domain-domain interactions from protein-protein interactions in the complex network conformation

Background As protein domains are functional and structural units of proteins, a large proportion of protein-protein interactions (PPIs) are achieved by domain-domain interactions (DDIs), many computational efforts have been made to identify DDIs from experimental PPIs since high throughput technologies have produced a large number of PPIs for different species. These methods can...

Up-Regulation of Intestinal Epithelial Cell Derived IL-7 Expression by Keratinocyte Growth Factor through STAT1/IRF-1, IRF-2 Pathway

Background Epithelial cells(EC)-derived interleukin-7 (IL-7) plays a crucial role in control of development and homeostasis of neighboring intraepithelial lymphocytes (IEL), and keratinocyte growth factor (KGF) exerts protective effects on intestinal epithelial cells and up-regulates EC-derived IL-7 expression through KGFR pathway. This study was to further investigate the...