Fine tuned exploration of evolutionary relationships within the protein universe

DOI10.1515/SAGMB-2019-0039MaRDI QIDQ2236693zbMATH OpenOpenAlexFDO

Authors Danilo Gullotto

Publication date 26 October 2021

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1515/sagmb-2019-0039

zbMATH Keywords

closed loopprotein networkLUCAco-independent evolutionary sitesintra-domain interactionssequence profile

Mathematics Subject Classification ID

Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20)

Recommendations

• Evolving protein interaction networks through gene duplication
• Walking through protein sequence space
• Structural relatedness via flow networks in protein sequence space
• Cooperative ``folding transition in the sequence space facilitates function-driven evolution of protein families
• Research in Computational Molecular Biology

Cites work

• Collective dynamics of `small-world' networks
• Fast unfolding of communities in large networks
• On Information and Sufficiency
• Probing the protein space for extending the detection of weak homology folds

Cited in

(4)

• Protein communication system: Evolution and genomic structure
• Modeling Dependence in Evolutionary Inference for Proteins
• A MODEL OF LARGE-SCALE PROTEOME EVOLUTION
• Protein evolution on partially correlated landscapes.

Describes a project that uses

Uses Software

• MEGA
• ClustalW
• Gephi
• PSI-BLAST
• BLAST
• TM-align

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