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Assessment of protein models with three-dimensional profiles
TLDR
It is shown that an effective test of the accuracy of a 3D protein model is a comparison of the model to its own amino-acid sequence, using a3D profile, computed from the atomic coordinates of the structure 3D profiles of correct protein structures match their own sequences with high scores, in contrast,3D profiles for protein models known to be wrong score poorly. Expand
The Database of Interacting Proteins: 2004 update
TLDR
This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Expand
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
The Database of Interacting Proteins (DIP: http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein-protein interactions. It provides the scientific community withExpand
A method to identify protein sequences that fold into a known three-dimensional structure.
TLDR
This 3D profile method is able to detect the structural similarity of the actins and 70- kilodalton heat shock proteins, even though these protein families share no detectable sequence similarity. Expand
VERIFY3D: assessment of protein models with three-dimensional profiles.
TLDR
Three-dimensional profiles computed from correct protein structures match their own sequences with high scores, and can be verified by its 3D profile, regardless of whether the model has been derived by X-ray, nuclear magnetic resonance (NMR), or computational procedures. Expand
Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
TLDR
It is discovered that exposure of cell or tissue lysates to a biotinylated isoxazole (b-isox) chemical precipitated hundreds of RNA-binding proteins with significant overlap to the constituents of RNA granules, offering a framework for understanding the function of LC sequences as well as an organizing principle for cellular structures that are not membrane bound. Expand
DIP: the Database of Interacting Proteins
The Database of Interacting Proteins (DIP; http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein-protein interactions. This database is intended to provide theExpand
Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.
TLDR
This work bridges structural genomics to structural biology with a procedure for determining protein complexes of previously unknown function from any organism with a sequenced genome and its entire procedure can be scaled to a genome-wide level. Expand
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.
TLDR
It is shown that proteins having matching or similar profiles strongly tend to be functionally linked, and this method of phylogenetic profiling allows us to predict the function of uncharacterized proteins. Expand
Analysis of membrane and surface protein sequences with the hydrophobic moment plot.
TLDR
An algorithm has been developed which identifies alpha-helices involved in the interactions of membrane proteins with lipid bilayers and which distinguishes them from helices in soluble proteins, and suggests four transmembrane helices and a surface-seeking helix in fragment B, the moiety known to have trans Membrane function. Expand
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