Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions

2016 ◽  
Vol 15 (7) ◽  
pp. 2123-2131 ◽  
Author(s):  
Te-Lun Mai ◽  
Geng-Ming Hu ◽  
Chi-Ming Chen
Keyword(s):  
Similarity Networks ◽  
Protein Similarity Networks

scholarly journals Pythoscape: a framework for generation of large protein similarity networks

2012 ◽  
Vol 28 (21) ◽  
pp. 2845-2846 ◽  
Author(s):  
Alan E. Barber ◽  
Patricia C. Babbitt
Keyword(s):  
Large Protein ◽  
Similarity Networks ◽  
Protein Similarity Networks

scholarly journals Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions

2017 ◽  
Vol 18 (S12) ◽  
Author(s):  
Xiaoxiong Zheng ◽  
Yang Wang ◽  
Kai Tian ◽  
Jiaogen Zhou ◽  
Jihong Guan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Multiple Protein ◽  
Similarity Networks ◽  
Protein Similarity Networks

scholarly journals Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis

2016 ◽  
Vol 113 (13) ◽  
pp. 3579-3584 ◽  
Author(s):  
Raphaël Méheust ◽  
Ehud Zelzion ◽  
Debashish Bhattacharya ◽  
Philippe Lopez ◽  
Eric Bapteste
Keyword(s):  
Functional Data ◽  
Genetic Information ◽  
Calvin Cycle ◽  
Carotenoid Biosynthesis ◽  
Photosynthetic Eukaryotes ◽  
Similarity Networks ◽  
Protein Similarity Networks ◽  
Oxygen Evolving ◽  
S Genes ◽  
Wide Swath

The integration of foreign genetic information is central to the evolution of eukaryotes, as has been demonstrated for the origin of the Calvin cycle and of the heme and carotenoid biosynthesis pathways in algae and plants. For photosynthetic lineages, this coordination involved three genomes of divergent phylogenetic origins (the nucleus, plastid, and mitochondrion). Major hurdles overcome by the ancestor of these lineages were harnessing the oxygen-evolving organelle, optimizing the use of light, and stabilizing the partnership between the plastid endosymbiont and host through retargeting of proteins to the nascent organelle. Here we used protein similarity networks that can disentangle reticulate gene histories to explore how these significant challenges were met. We discovered a previously hidden component of algal and plant nuclear genomes that originated from the plastid endosymbiont: symbiogenetic genes (S genes). These composite proteins, exclusive to photosynthetic eukaryotes, encode a cyanobacterium-derived domain fused to one of cyanobacterial or another prokaryotic origin and have emerged multiple, independent times during evolution. Transcriptome data demonstrate the existence and expression of S genes across a wide swath of algae and plants, and functional data indicate their involvement in tolerance to oxidative stress, phototropism, and adaptation to nitrogen limitation. Our research demonstrates the “recycling” of genetic information by photosynthetic eukaryotes to generate novel composite genes, many of which function in plastid maintenance.

Clustering and visualizing similarity networks of membrane proteins

2015 ◽  
Vol 83 (8) ◽  
pp. 1450-1461 ◽  
Author(s):  
Geng-Ming Hu ◽  
Te-Lun Mai ◽  
Chi-Ming Chen
Keyword(s):  
Membrane Proteins ◽  
Similarity Networks

scholarly journals Diversity of GPI-anchored fungal adhesins

2020 ◽  
Vol 401 (12) ◽  
pp. 1389-1405
Author(s):  
Lars-Oliver Essen ◽  
Marian Samuel Vogt ◽  
Hans-Ulrich Mösch
Keyword(s):  
Cell Wall ◽  
Cell Surface ◽  
Bioinformatics Analysis ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Growth Forms ◽  
Similarity Networks ◽  
Fungal Adhesins ◽  
Sequence Similarity Networks ◽  
Successful Colonization

AbstractSelective adhesion of fungal cells to one another and to foreign surfaces is fundamental for the development of multicellular growth forms and the successful colonization of substrates and host organisms. Accordingly, fungi possess diverse cell wall-associated adhesins, mostly large glycoproteins, which present N-terminal adhesion domains at the cell surface for ligand recognition and binding. In order to function as robust adhesins, these glycoproteins must be covalently linkedto the cell wall via C-terminal glycosylphosphatidylinositol (GPI) anchors by transglycosylation. In this review, we summarize the current knowledge on the structural and functional diversity of so far characterized protein families of adhesion domains and set it into a broad context by an in-depth bioinformatics analysis using sequence similarity networks. In addition, we discuss possible mechanisms for the membrane-to-cell wall transfer of fungal adhesins by membrane-anchored Dfg5 transglycosidases.

scholarly journals MeFSAT: A curated natural product database specific to secondary metabolites of medicinal fungi

2020 ◽  
Author(s):  
R.P. Vivek-Ananth ◽  
Ajaya Kumar Sahoo ◽  
Kavyaa Kumaravel ◽  
Karthikeyan Mohanraj ◽  
Areejit Samal
Keyword(s):  
Secondary Metabolites ◽  
Physicochemical Properties ◽  
Natural Product ◽  
Chemical Space ◽  
Chemical Structures ◽  
Therapeutic Uses ◽  
Natural Product Library ◽  
Medicinal Fungi ◽  
Similarity Networks ◽  
Shape Complexity

AbstractFungi are a rich source of secondary metabolites which constitutes a valuable and diverse chemical space of natural products. Medicinal fungi have been used in traditional medicine to treat human ailments for centuries. To date, there is no devoted resource on secondary metabolites and therapeutic uses of medicinal fungi. Such a dedicated resource compiling dispersed information on medicinal fungi across published literature will facilitate ongoing efforts towards natural product based drug discovery. Here, we present the first comprehensive manually curated database on Medicinal Fungi Secondary metabolites And Therapeutics (MeFSAT) that compiles information on 184 medicinal fungi, 1830 secondary metabolites and 149 therapeutics uses. Importantly, MeFSAT contains a non-redundant in silico natural product library of 1830 secondary metabolites along with information on their chemical structures, computed physicochemical properties, drug-likeness properties, predicted ADMET properties, molecular descriptors and predicted human target proteins. By comparing the physicochemical properties of secondary metabolites in MeFSAT with other small molecules collections, we find that fungal secondary metabolites have high stereochemical complexity and shape complexity similar to other natural product libraries. Based on multiple scoring schemes, we have filtered a subset of 228 drug-like secondary metabolites in MeFSAT database. By constructing and analyzing chemical similarity networks, we show that the chemical space of secondary metabolites in MeFSAT is highly diverse. The compiled information in MeFSAT database is openly accessible at: https://cb.imsc.res.in/mefsat/.

scholarly journals Community detection in sequence similarity networks based on attribute clustering

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0178650
Author(s):  
Janamejaya Chowdhary ◽  
Frank E. Löffler ◽  
Jeremy C. Smith
Keyword(s):  
Community Detection ◽  
Sequence Similarity ◽  
Similarity Networks ◽  
Sequence Similarity Networks ◽  
Attribute Clustering
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