Protein is a very important part of a cell. It carries out its duties as specified by the information encoded in genes. Proteins interact with each other to carry out different biological functions. Information about these interactions will help a lot in understanding different diseases. Different classifiers have been used till now to classify the protein-protein interactions. Some of the clas...

Using beta-hairpin model systems, we have investigated the role of aromatic interactions in providing selectivity to protein folding and protein-protein interactions. In particular, we have explored the role of cation-p and amide-p interactions and their role in controlling proteinprotein interactions with post-translationally modified proteins. Specific modifications that have been studied are...

Our Mouse Encyclopedia Project, which performs exhaustive collection and sequencing of all mRNA species expressed in mouse, successfully collected more than 70,000 different kind of cDNA clones classifiable by 3’-end sequence tags. By Using those clones, we are completing sequence of the isolated cDNA clones in concurrent manner, which piled up to over 10,000 sequences. This number tells that o...

Cellular processes are the interaction of multiple proteins, genomic sites, RNAs, small molecules, and their complexes. The set of these interactions and their contexts provide biological understanding of functionality beyond single-gene annotation. Biological networks have emerged as the dominant method of communicating, modeling, and understanding cellular processes and pathways. Computationa...

TEL–platelet-derived growth factor– receptor (TEL-PDGF R) is expressed in chronic myelomonocytic leukemias associated with t(5;12)(q33;p13), and the fusion tyrosine kinase retains a conserved WW-like domain in the PDGF R autoinhibitory juxtamembrane region. Here we report that mutation of the 2 conserved tryptophan residues of the WW-like domain has opposing effects on TELPDGF R kinase activati...

The vast number of published medical documents is considered a vital source for relationship discovery. This paper presents a statistical unsupervised system, called BioNoculars, for extracting protein-protein interactions from biomedical text. BioNoculars uses graph-based mutual reinforcement to make use of redundancy in data to construct extraction patterns in a domain independent fashion. Th...

Copyright: © 2012 Nebel JC. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Following the completion of the Human Genome Project, came the humbling discovery that humans possess barely more protein-coding gene...

State-of-the-art methods for proteinprotein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to ...

With the exception of the divergent β4 and β8 chains, the integrin β subunit cytoplasmic domains are short and highly conserved sequences. Consensus motifs are found among the different cytoplasmic β chains. Experiments using chimeric receptors demonstrated that the 47 amino acids of the β1 subunit cytoplasmic domain contain sufficient information to target integrins to adhesion plaques. Three ...

Protein-protein interactions (PPI) refer to the associations between proteins and the study of these associations. Recent studies show that a network representation of proteins provides a more accurate model of biological systems and process compared to conventional pair-wise analysis. Many graph analysis has been proposed to the network for interactions prediction, pathway discovery and comple...