Filters








58,344 Hits in 4.8 sec

Computational prediction of host-pathogen protein–protein interactions

Matthew D. Dyer, T. M. Murali, Bruno W. Sobral
2007 Computer applications in the biosciences : CABIOS  
One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins.  ...  We show that pairs of human proteins we predict to interact with the same Plasmodium protein are close to each other in the human PPI network and that Plasmodium pairs predicted to interact with same human  ...  This work was supported by Department of Defense grant #DAAD 13-02-C-0018 to B.S., PI.  ... 
doi:10.1093/bioinformatics/btm208 pmid:17646292 fatcat:lbt2lhvwzbbp5oahr7ct64o46y

Computational approaches for prediction of pathogen-host protein-protein interactions

Esmaeil Nourani, Farshad Khunjush, Saliha Durmuş
2015 Frontiers in Microbiology  
Keywords: protein-protein interaction, pathogen-host interaction (PHI), computational PHI prediction, machine learning, data mining www.frontiersin.org February 2015 | Volume 6 | Article 94 | 1 Nourani  ...  Molecular interactions between pathogens and their hosts are the key parts of the infection mechanisms.  ...  To apply this idea to a pathogen-host system, they identify domains in every host and pathogen proteins and compute the interaction probability for each pair of host and pathogen proteins that contain  ... 
doi:10.3389/fmicb.2015.00094 pmid:25759684 pmcid:PMC4338785 fatcat:wudzxofahzdrnpruzkjmclyjhq

Issues in performance evaluation for host–pathogen protein interaction prediction

Wajid Arshad Abbasi, Fayyaz Ul Amir Afsar Minhas
2016 Journal of Bioinformatics and Computational Biology  
A number of machine learning based methods for predicting host-pathogen interactions (HPIs) have been proposed in the literature.  ...  The study of protein-protein interactions (PPIs) between host and pathogen proteins is important for understanding the underlying mechanism of infectious diseases and for developing novel therapeutic solutions  ...  Abbasi is supported by a grant from Higher Education Commission (HEC) of Pakistan.  ... 
doi:10.1142/s0219720016500116 pmid:26932275 fatcat:d3qsser5pfc65dexx5m4jafoui

Computational prediction of host-pathogen protein-protein interactions

Ibrahim Ahmed
2017 unpublished
Computational prediction of host-pathogen protein-protein interactions I.H.I Ahmed (Ibrahim) Supervised machine learning approaches have been applied successfully to the prediction of protein-protein interactions  ...  The primary aim of this bioinformatics thesis was to develop a binary classifier with an appropriate feature set for host-pathogen protein-protein interaction prediction using published human-Hepatitis  ...  On the other hand computational methods for predicting host-pathogen protein protein interaction has not received much attention due to the difficulty of experimental validation.  ... 
fatcat:fvrmv45dgbahvgh2tzsg5i5on4

Protein–Protein Interactions [chapter]

2013 Encyclopedia of Biophysics  
One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins.  ...  We show that pairs of human proteins we predict to interact with the same Plasmodium protein are close to each other in the human PPI network and that Plasmodium pairs predicted to interact with same human  ...  This work was supported by Department of Defense grant #DAAD 13-02-C-0018 to B.S., PI.  ... 
doi:10.1007/978-3-642-16712-6_100832 fatcat:pu3gxqaoufgj5a53tecn6j7lim

Protein–­Protein Interactions [chapter]

2015 Techniques in Genetic Engineering  
One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins.  ...  We show that pairs of human proteins we predict to interact with the same Plasmodium protein are close to each other in the human PPI network and that Plasmodium pairs predicted to interact with same human  ...  This work was supported by Department of Defense grant #DAAD 13-02-C-0018 to B.S., PI.  ... 
doi:10.1201/b18484-7 fatcat:dbze5mhw4bc7ji2p5guo7x6glu

Protein-Protein Interactions [chapter]

2008 Integrated Molecular and Cellular Biophysics  
One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins.  ...  We show that pairs of human proteins we predict to interact with the same Plasmodium protein are close to each other in the human PPI network and that Plasmodium pairs predicted to interact with same human  ...  This work was supported by Department of Defense grant #DAAD 13-02-C-0018 to B.S., PI.  ... 
doi:10.1007/978-1-4020-8268-9_8 fatcat:7ojxeije6zbq5caqcv22ju4zsm

An Integrative Computational Approach for the Prediction of Human-Plasmodium Protein-Protein Interactions

Kais Ghedira, Yosr Hamdi, Abir El Béji, Houcemeddine Othman, Jane Hanrahan
2020 BioMed Research International  
Most of these cross-talks are mediated via protein-protein interactions between the host and the pathogen (HP-PPI).  ...  Thus, it is essential to know how some pathogens interact with their hosts to understand the mechanism of infections.  ...  It was also partially supported by the European project PHINDaccess: Strengthening Omics data analysis capacities in pathogen-host interaction (Grant agreement ID: 811034).  ... 
doi:10.1155/2020/2082540 pmid:33426052 pmcid:PMC7771252 fatcat:rtzlxvvrhndnths2pna5neuiqu

Genome-scale host-pathogen prediction for non-medical microbes [article]

Mais Ammari, Cathy Gresham, Fiona Maree McCarthy, Bindu Nanduri
2022 bioRxiv   pre-print
Evaluation of predicted HPIs demonstrates that the host proteins predicted to be involved in pathogen interactions include hubs and bottlenecks in the network, as reported in curated host proteins.  ...  Network studies of host-pathogen interactions (HPI) are critical in understanding the mechanisms of pathogenesis. However, accessible HPI data for agriculturally important pathogens are limited.  ...  host-pathogen protein interactions, to help evaluate the quality of the predictions.  ... 
doi:10.1101/2022.07.20.500869 fatcat:avhgpfd7ojaarpmorhunb3cn6i

Toward a three-dimensional view of protein networks between species

Eric A. Franzosa, Sara Garamszegi, Yu Xia
2012 Frontiers in Microbiology  
Here, we review the nascent field of between-species structural systems biology, focusing on interactions between host and pathogens such as viruses.  ...  Recent progress in structural biology, systems biology, and computational biology has enabled accurate and large-scale construction of 3D structural models of nodes and edges for protein-protein interaction  ...  A key computational challenge is the development of unified, predictive models of how host and pathogens interact through integration of these datasets.  ... 
doi:10.3389/fmicb.2012.00428 pmid:23267356 pmcid:PMC3528071 fatcat:i5fwemjssbdj7he7y75pfps4wq

Predicting Protein–Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches

Cunjian Zheng, Yuan Liu, Fangnan Sun, Lingxia Zhao, Lida Zhang
2021 Frontiers in Plant Science  
In this study, we presented a computational framework for predicting plant–pathogen PPIs based on structural information.  ...  The network provided a global map to help accelerate the identification of blast resistance genes and advance our understanding of plant–pathogen interactions.  ...  The results indicated its robust FIGURE 1 | A computational framework for predicting protein-protein interactions (PPIs) between host and pathogen.  ... 
doi:10.3389/fpls.2021.690124 fatcat:x2tkk5rjtna3xllxijpc5jmaxe

Towards Biological Sequence Data Service with Insights

Huaming Chen, Jun Shen, Lei Wang, Chi-Hung Chi
2018 2018 IEEE International Conference on Big Data (Big Data)  
Specifically, we present this service in a framework for studies on host-pathogen interactions. The design of this framework aims to improve the understanding of host-pathogen interactions.  ...  Specifically, we present this service in a framework for studies on host-pathogen interactions. The design of this framework aims to improve the understanding of host-pathogen interactions.  ...  supported by the scholarship from the China Scholarship Council (CSC) and Faculty Strategic Investments Grant for DP 2019 development, while the first author pursues his PhD degree in the University of  ... 
doi:10.1109/bigdata.2018.8622194 dblp:conf/bigdataconf/ChenSWC18 fatcat:sjlawudlojdqbepefm5r6mahoq

Host-pathogen protein interactions predicted by comparative modeling

Fred P. Davis, David T. Barkan, Narayanan Eswar, James H. McKerrow, Andrej Sali
2007 Protein Science  
Here, we present and apply a computational whole-genome protocol that generates testable predictions of host-pathogen protein interactions.  ...  and (3) analysis of the functional properties of the human proteins predicted to interact with pathogen proteins, demonstrating an enrichment for functionally relevant host-pathogen interactions.  ...  Boothroyd (Stanford) for their help in building the set of known host-pathogen protein interactions. We thank D. Shanmugam (U. Penn) for collating the protein sequences analyzed and U.  ... 
doi:10.1110/ps.073228407 pmid:17965183 pmcid:PMC2222825 fatcat:trhw4zvo7vedpc2khxx3yufhzq

Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches

Sitanshu S Sahu, Tyler Weirick, Rakesh Kaundal
2014 BMC Bioinformatics  
Hence, there is a need for developing efficient computational models to predict the interaction between host and pathogen in a genome scale, and find novel candidate effectors and/or their targets.  ...  of the molecular dynamics of plant-pathogen interactions.  ...  This article has been published as part of BMC Bioinformatics Volume 15 Supplement 11, 2014: Proceedings of the 11th Annual MCBIOS Conference.  ... 
doi:10.1186/1471-2105-15-s11-s13 pmid:25350354 pmcid:PMC4251041 fatcat:bwx2mzvhira4lnripygdomwryq

Inter-Species/Host-Parasite Protein Interaction Predictions Reviewed

Jumoke Soyemi, Itunnuoluwa Isewon, Jelili Oyelade, Ezekiel Adebiyi
2018 Current Bioinformatics  
This study looks at various computational methods used in literature for host-parasite/inter-species protein-protein interaction predictions with the hope of getting a better insight into computational  ...  Tabulations of studies that carried out host-parasite/inter-species protein interaction predictions were performed, analyzing their predictive methods, filters used, potential protein-protein interactions  ...  Computational method of identifying host-parasite protein interactions became popular because of this limitation in experimental method.  ... 
doi:10.2174/1574893613666180108155851 pmid:31496926 pmcid:PMC6691774 fatcat:qybbjhnckzfkzp7ng3nq3se4ey
« Previous Showing results 1 — 15 out of 58,344 results