Advertisement

Topics

PPICurator: a tool for extracting comprehensive protein-protein interaction information.

07:00 EST 6th December 2018 | BioPortfolio

Summary of "PPICurator: a tool for extracting comprehensive protein-protein interaction information."

PPI extraction through biological literature curation has been widely employed for proteome analysis. There is a strong need for a tool that can assist researchers in extracting comprehensive PPI information through literature curation, which is critical in research on protein, e.g., construction of protein interaction network, identification of protein signaling pathway and discovery of meaningful protein interaction. However, most of current tools can only extract PPI relations. None of them are capable of extracting other important PPI information, such as interaction directions, effects and functional annotations. To address these issues, this paper proposes PPICurator, a novel tool for extracting comprehensive PPI information with a variety of logic and syntax features based on a new support vector machine (SVM) classifier. PPICurator provides a friendly web-based user interface. It is a platform that automates the extraction of comprehensive PPI information through literature, including PPI relations, as well as their confidential scores, interaction directions, effects and functional annotations. Thus, PPICurator is more comprehensive than state-of-the-art tools. Moreover, it outperforms state-of-the-art tools in the accuracy of PPI relation extraction measured by F-score and recall on the widely-used open datasets. PPICurator is available at https://ppicurator.hupo.org.cn. This article is protected by copyright. All rights reserved.

Affiliation

Journal Details

This article was published in the following journal.

Name: Proteomics
ISSN: 1615-9861
Pages: e1800291

Links

DeepDyve research library

PubMed Articles [29047 Associated PubMed Articles listed on BioPortfolio]

LPGNMF: Predicting Long Non-coding RNA and Protein Interaction Using Graph Regularized Nonnegative Matrix Factorization.

Long non-coding RNAs (lncRNA) play crucial roles in a variety of biological processes and complex diseases. Massive studies have indicated that lncRNAs interact with related proteins to exert regulati...

Unique Physicochemical Patterns of Residues in Protein-Protein Interfaces.

Protein-protein interactions can be characterized by high-resolution structures of complexes, from which diverse features of the interfaces can be derived. For the majority of protein-protein interact...

Ubiquitin-Activated Interaction Traps (UBAITs): Tools for Capturing Protein-Protein Interactions.

UBAITs (Ubiquitin-Activated Interaction Traps) are reagents that capitalize on the biochemistry of the ubiquitin system to covalently trap transient protein-protein interactions. UBAITs consist of an ...

Protein-protein interactions of human viruses.

Viruses infect their human hosts by a series of interactions between viral and host proteins, indicating that detailed knowledge of such virus-host interaction interfaces are critical for our understa...

Scop3D: online visualization of mutation rates on protein structure.

Scop3D is a tool that automatically annotates protein structure with sequence conservation starting from a set of protein sequence variants. Here, we present a complete upgrade and rewrite of Scop3D. ...

Clinical Trials [8106 Associated Clinical Trials listed on BioPortfolio]

Real-time Amino Acid Profiling

This study was designed to obtain information about the effect of new combinations of dairy proteins, in small servings with high protein concentrations, on postprandial amino acid kinetic...

Role of Dietary Protein Intake in Elderly Adults

The investigators examined the effects of dietary protein intake in a mixed meal at two levels of protein amount on whole body protein metabolisms in older adults.

Replacing Protein Via Enteral Nutrition in a Stepwise Approach in Critically Ill Patients

In this study, we will explore the feasibility of doing a randomized controlled trial in our Intensive care department, King Abdulaziz Medical City, Riyadh which will test a two-step appro...

Meat Protein and Calcium: Do They Interact Synergistically or Antagonistically?

The primary objective is to determine whether meat interacts positively with calcium to improve calcium retention. The secondary objective is to determine whether any interaction between d...

Dietary Protein Requirement of Elderly Men and Women

The purpose of this study was to assess the effect of age on the estimated average requirement and adequate allowance for dietary protein.

Medical and Biotech [MESH] Definitions

Protein interaction domains of about 70-90 amino acid residues, named after a common structure found in PSD-95, Discs Large, and Zona Occludens 1 proteins. PDZ domains are involved in the recruitment and interaction of proteins, and aid the formation of protein scaffolds and signaling networks. This is achieved by sequence-specific binding between a PDZ domain in one protein and a PDZ motif in another protein.

Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.

Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.

Methods for determining interaction between proteins.

A minichromosome maintenance protein that is a key component of the six member MCM protein complex. In addition, interaction of this protein with cyclin A results in its recruitment to CENTROSOMES where it may play a role in controlling centrosome reduplication.

Advertisement
Quick Search
Advertisement
Advertisement

 


DeepDyve research library

Relevant Topics

Nutrition
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...

Biological Therapy
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...


Searches Linking to this Article