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Weiyi Zhang







C++ Programming 

  1.  Effective and More Effective C++. (more...)
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Python Programming

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Documents and notes 

Paper abstracts

  1.   PDZ paper abstracts. (more...)

Work Notes

  1. Sending Signal Dynamically. (Smock RG, Gierasch LM (2009) Sending signals dynamically. Science 324: 198-203.)

    It is increasingly apparent that signaling relies on the intrinsic dynamic properties of proteins and that proteins relay signals by shifting among different fluctuating energy states in response to one or more inputs. (more...)

  2. Reassessing a sparse energetic network within a single protein domain. (Chi CN, Elfstrom L, Shi Y, Snall T, Engstrom A, et al. (2008) )

    Our results reveal that the sparse energetic network in PSD95 PDZ3 is not affecting ligand binding more than non-network residues. The observed coupling energies for binding can be explained by a model where distance is correlated with coupling (8), as shown previously for the barnase–barstar complex (15) and Staphylococcal nuclease (8, 16). Thus, statistical coupling inferred from multiple sequence alignment is not necessarily a true reporter of functional coupling. (more...)

  3. Evolutionarily conserved pathways of energetic connectivity in protein families. (Lockless SW, Ranganathan R (1999) Science 286: 295-299.)

    For mapping energetic interactions in proteins, a technique was developed that uses evolutionary data for a protein family to measure statistical interactions between amino acid positions. For the PDZ domain family, this analysis predicted a set of energetically coupled positions for a binding site residue that includes unexpected long-range interactions. Mutational studies conÞrm these predictions, demonstrating that the statistical energy function is a good indicator of thermodynamic coupling in proteins. Sets of interacting residues form connected pathways through the protein fold that may be the basis for efÞcient energy conduction within proteins. (more...)

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