Protein Pockets: Inventory, Shape, and Comparison
نویسندگان
چکیده
منابع مشابه
Protein Pockets: Inventory, Shape, and Comparison
The shape of the protein surface dictates what interactions are possible with other macromolecules, but defining discrete pockets or possible interaction sites remains difficult. First, there is the problem of defining the extent of the pocket. Second, one has to characterize the shape of each pocket. Third, one needs to make quantitative comparisons between pockets on different proteins. An el...
متن کاملCavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets
We analyzed 78 binding pockets of the human urokinase plasminogen activator (uPA) catalytic domain extracted from a data set of crystallized uPA-ligand complexes. These binding pockets were computed with an original geometric method that does NOT involve any arbitrary parameter, such as cutoff distances, angles, and so on. We measured the deviation from convexity of each pocket shape with the p...
متن کاملFast prediction and visualization of protein binding pockets with PASS
PASS (Putative Active Sites with Spheres) is a simple computational tool that uses geometry to characterize regions of buried volume in proteins and to identify positions likely to represent binding sites based upon the size, shape, and burial extent of these volumes. Its utility as a predictive tool for binding site identification is tested by predicting known binding sites of proteins in the ...
متن کاملA new method for rapid comparison of protein binding pockets by capturing spatial distributions
Efficient determination of structural similarities between protein binding pockets is an important challenge in computational chemistry. A degree of similarity in the mutual comparison is often estimated in terms of graphs and by calculating a metric such as the maximum shared common subgraph. Cavbase [1] was developed as a tool for the automatic detection, storage and classification of putativ...
متن کاملAnatomy of protein pockets and cavities: Measurement of binding
Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structurebased ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings, ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Information and Modeling
سال: 2010
ISSN: 1549-9596,1549-960X
DOI: 10.1021/ci900397t