Advanced search    

Search: authors:"Sheng Wang"

54 papers found.
Use AND, OR, NOT, +word, -word, "long phrase", (parentheses) to fine-tune your search.

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...

Arabidopsis ubiquitin-conjugating enzyme UBC22 is required for female gametophyte development and likely involved in Lys11-linked ubiquitination

Protein ubiquitination is critical for numerous processes in eukaryotes. The ubiquitin-conjugating enzyme (E2) is required for ubiquitination. The Arabidopsis genome has approximately 37 E2 genes, but in vivo functions for most of them remain unknown. In this study we observed that knockout mutants of Arabidopsis UBC22 had much-reduced silique length and seed number, with nearly...

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...

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that...

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...

Fuzzy optimization for detecting enzyme targets of human uric acid metabolism

Motivation: Mathematical modeling and optimization have been used for detecting enzyme targets in human metabolic disorders. Such optimal drug design methods are generally differentiated as two stages, identification and decision-making, to find optimal targets. We developed a unified method named fuzzy equal metabolic adjustment to formulate an optimal enzyme target design...

Protein threading using context-specific alignment potential

Motivation: Template-based modeling, including homology modeling and protein threading, is the most reliable method for protein 3D structure prediction. However, alignment errors and template selection are still the main bottleneck for current template-base modeling methods, especially when proteins under consideration are distantly related. Results: We present a novel context...

Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling

To understand the physiological and molecular mechanisms underlying seedling salt tolerance in rice (Oryza sativa L.), the phenotypic, metabolic, and transcriptome responses of two related rice genotypes, IR64 and PL177, with contrasting salt tolerance were characterized under salt stress and salt+abscisic acid (ABA) conditions. PL177 showed significantly less salt damage, lower...

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...

Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling

Sheng Wang 0 Jian Peng 0 Jinbo Xu 0 Associate Editor: Anna Tramontano 0 Toyota Technological Institute at Chicago , IL 60637, USA Motivation: Building an accurate alignment of a large set of

Management of Chronic Hepatitis B e Antigen–Negative Disease: Another Step Forward

George K. K. Lau () 0 Fu-Sheng Wang 0 0 Institute of Translational Hepatology , Beijing, China - Chronic hepatitis B (CHB) infection is a global health problem affecting more than 2 billion people

Lynx: a database and knowledge extraction engine for integrative medicine

We have developed Lynx (http://lynx.ci.uchicago.edu)—a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35...

Epidemiology46. Low Back Pain and Occupational Risk Factors Among Coal Miners in China

Background: Although low back pain (LBP) is one of the common reasons for absenteeism in the coal mining industry, there is little epidemiological data about LBP in workers in the developing countries. The purpose of the present study is to determine the prevalence of LBP in coal miners in China and to examine associations between work-related factors and LBP.

Inference of biochemical network models in S-system using multiobjective optimization approach

Pang-Kai Liu 0 Feng-Sheng Wang 0 Associate Editor: John Quackenbush 0 Department of Chemical Engineering, National Chung Cheng University , Chiayi 621-02, Taiwan , ROC Motivation: The inference of

4-(Methylnitro-Samino)-1-(3-Pyridyl)-1-Butanone Induces CRM1-Dependent P53 Nuclear Accumulation in Human Bronchial Epithelial Cells

4-(Methylnitro-samino)-1-(3-pyridyl)-1-butanone (NNK), a known tobacco-specific human lung carcinogen, is notorious for causing DNA damage. The tumor suppressor gene p53 has multiple functions in response to DNA damage. Besides being regulated by posttranslational modifications (PTMs), p53 function is modulated by nucleocytoplasmic shuttling factors (NSFs). In this study, the...