Alexandra Shulman-Peleg

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Cloud storage systems are becoming increasingly popular. A promising technology that keeps their cost down is <i>deduplication</i>, which stores only a single copy of repeating data. <i>Client-side deduplication</i> attempts to identify deduplication opportunities already at the client and save the bandwidth of uploading copies of existing files to the(More)
As the volume of data increases, so does the demand for online storage services, from simple backup services to cloud storage infrastructures. Although deduplication is most effective when applied across multiple users, cross-user deduplication has serious privacy implications. Some simple mechanisms can enable cross-user deduplication while greatly(More)
Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may(More)
Recognition of binding patterns common to a set of protein structures is important for recognition of function, prediction of binding, and drug design. We consider protein binding sites represented by a set of 3D points with assigned physico-chemical and geometrical properties important for protein-ligand interactions. We formulate the multiple binding site(More)
Analysis of protein-ligand complexes and recognition of spatially conserved physico-chemical properties is important for the prediction of binding and function. Here, we present two webservers for multiple alignment and recognition of binding patterns shared by a set of protein structures. The first webserver, MultiBind(More)
Protein-protein interfaces are regions between 2 polypeptide chains that are not covalently connected. Here, we have created a nonredundant interface data set generated from all 2-chain interfaces in the Protein Data Bank. This data set is unique, since it contains clusters of interfaces with similar shapes and spatial organization of chemical functional(More)
We present a novel computational method, MultiBind, for recognition of binding patterns common to a set of protein structures. It is the first method which performs a multiple alignment between protein binding sites in the absence of overall sequence, fold or binding partner similarity. MultiBind recognizes common spatial arrangements of physico-chemical(More)
Cloud storage services commonly use deduplication, which eliminates redundant data by storing only a single copy of each file or block. Deduplication reduces the space and bandwidth requirements of data storage services, and is most effective when applied across multiple users, a common practice by cloud storage offerings. We study the privacy implications(More)
The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein function. Comprehension of protein function at its most basic level requires understanding of molecular interactions. Currently, it is becoming(More)