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PlasmoID: A P. falciparum Information Discovery Tool PlasmoID:恶性疟原虫信息发现工具

Silico Biol. Pub Date : 1900-01-01 DOI: 10.3233/ISB-2009-0403

Aditya Rao, S. Yeleswarapu, Gudladona Raghavendra, Rajgopal Srinivasan, Gopalakrishnan Bulusu

{"title":"PlasmoID: A P. falciparum Information Discovery Tool","authors":"Aditya Rao, S. Yeleswarapu, Gudladona Raghavendra, Rajgopal Srinivasan, Gopalakrishnan Bulusu","doi":"10.3233/ISB-2009-0403","DOIUrl":"https://doi.org/10.3233/ISB-2009-0403","url":null,"abstract":"Plasmodium falciparum is the parasite responsible for more than 90% of deaths that occur due to malaria. Organization and mining of 'omic' (genomic, proteomic, transcriptomic, interactomic) data can improve our understanding of P. falciparum biology and help in the fight against malaria. PlasmoID (Plasmodium Information Discovery) is a tool developed for the dynamic exploration of the parasite's 'omic' landscape. Diverse computational and curated P. falciparum protein-protein interaction datasets, as well as binary relationships involving protein-small molecule entities, manually curated protein-protein relationships derived from the published literature and protein-protein interactions based on metabolic pathways are included in the PlasmoID database. The graphical user interface is designed as a plug-in to Cytoscape, an open-source network visualization tool. Important features of this plug-in include a synchronized tabular representation of any network loaded on the canvas, ability to find the shortest path between a pair of nodes in the database, search and expansion of entities from the database, and the ability to add new entities to the database through the interface. Malaria researchers can now seamlessly interrogate heterogeneous 'omic' datasets as well as add proprietary data to generate and visualize P. falciparum pathway and cell process network models. PlasmoID can be downloaded from http://pfalciparum.atc.tcs.com/PlasmoID.","PeriodicalId":332777,"journal":{"name":"Silico Biol.","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126567991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Conformational Dynamics and Thermal Stabilities of the αβ-Tubulin Dimer: A Molecular Dynamics Simulation Study αβ-微管蛋白二聚体的构象动力学和热稳定性:分子动力学模拟研究

Silico Biol. Pub Date : 1900-01-01 DOI: 10.3233/ISB-2009-0404

Xiaomin Wu, Gang Yang, Y. Zu, Zhiwei Yang, Lijun Zhou

{"title":"Conformational Dynamics and Thermal Stabilities of the αβ-Tubulin Dimer: A Molecular Dynamics Simulation Study","authors":"Xiaomin Wu, Gang Yang, Y. Zu, Zhiwei Yang, Lijun Zhou","doi":"10.3233/ISB-2009-0404","DOIUrl":"https://doi.org/10.3233/ISB-2009-0404","url":null,"abstract":"Molecular dynamics simulations were employed to study the conformational dynamics and thermal stabilities of the large alphabeta-tubulin dimer systems under various conditions. The alphabeta-tubulin dimer at ambient and cryogenic temperatures remains stable around the native conformations, and the water solvent molecules tend to stabilize the native conformations through the formation of complex hydrogen-bonding networks. The elevation of temperature severely destroys the native conformations and the bioactivities, especially in aqueous solution. It was caused by the lack of intra- and inter-molecular interactions and the decrease of water polarity at higher temperatures. The conformational analysis of the selected segment (beta15-QIGAKFWEVIS) provides detailed information on the whole proteins. It was revealed that the local structures of proteins at ambient and cryogenic temperatures have obvious differences albeit the overall structures are close to each other. The selected segments under high temperatures are dominated by random coils instead of native helix at ambient and cryogenic temperatures,accompanied by more diversities and faster conversions of conformations. In addition, the temperature or/and the solvent are capable of altering the secondary structures and further the conformations of the segments and the whole proteins. At ambient temperatures, the water solvent helps the proteins to achieve the native conformation with bioactivities. Different from the corresponding segments in proteins, the truncated peptides are endowed with higher structural flexibilities and characterized by random coils even at ambient temperatures, along with the disappearance of helical hydrogen bonds.","PeriodicalId":332777,"journal":{"name":"Silico Biol.","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132438258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4