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Flexibility of -helices: Results of a statistical analysis of database protein structures
Eldon G. Emberly, Ranjan Mukhopadhyay, Ned S. Wingreen +1
-helices stand out as common and relatively invariant secondary structural elements of proteins. However, -helices are not rigid bodies and their deformations can be signific…
Statistical mechanics of RNA folding: importance of alphabet size
Ranjan Mukhopadhyay, Eldon Emberly, Chao Tang +1
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between t…
Designability of alpha-helical Proteins
Eldon Emberly, Ned Wingreen, Chao Tang
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a give…
The Designability of Protein Structures: A Lattice-Model Study using the Miyazawa-Jernigan Matrix
Hao Li, Chao Tang, Ned Wingreen
We study the designability of all compact 3x3x3 and 6x6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequen…