Walking through protein sequence space

DOI10.1016/J.JTBI.2006.07.027MaRDI QIDQ2209048zbMATH OpenOpenAlexWikidataFDO

Authors Zakharia M. Frenkel, Edward N. Trifonov

Publication date 28 October 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2006.07.027

zbMATH Keywords

protein evolutionconserved sequence/structure modulesprotein sequence spacesequence space walk

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Recommendations

• An \textit{in silico} exploration of the neutral network in protein sequence space
• Evolutionary Walks on Rugged Landscapes
• Protein evolution on partially correlated landscapes.
• Natural vs. random protein sequences: discovering combinatorics properties on amino acid words
• Cooperative ``folding transition in the sequence space facilitates function-driven evolution of protein families

Cites work

• scientific article; zbMATH DE number 2084315 (Why is no real title available?)
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.

Cited in

(7)

• Cooperative ``folding transition in the sequence space facilitates function-driven evolution of protein families
• Structural relatedness via flow networks in protein sequence space
• Protein space: a natural method for realizing the nature of protein universe
• Fine tuned exploration of evolutionary relationships within the protein universe
• Protein sequence and structure: is one more fundamental than the other?
• An \textit{in silico} exploration of the neutral network in protein sequence space
• Equivalent genomic (proteomic) sequences and semigroups

Describes a project that uses

Uses Software

• Pajek
• PSI-BLAST
• BLAST

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