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Detection of multiscale pockets on protein surfaces using mathematical morphology
Proteins, structure, function, and bioinformatics, 2010-04, Vol.78 (5), p.1195-1211
Kawabata, Takeshi
2010
Details
Autor(en) / Beteiligte
Kawabata, Takeshi
Titel
Detection of multiscale pockets on protein surfaces using mathematical morphology
Ist Teil von
Proteins, structure, function, and bioinformatics, 2010-04, Vol.78 (5), p.1195-1211
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2010
Link zum Volltext
Quelle
Wiley Online Library Journals Frontfile Complete
Beschreibungen/Notizen
Detection of pockets on protein surfaces is an important step toward finding the binding sites of small molecules. In a previous study, we defined a pocket as a space into which a small spherical probe can enter, but a large probe cannot. The radius of the large probes corresponds to the shallowness of pockets. We showed that each type of binding molecule has a characteristic shallowness distribution. In this study, we introduced fundamental changes to our previous algorithm by using a 3D grid representation of proteins and probes, and the theory of mathematical morphology. We invented an efficient algorithm for calculating deep and shallow pockets (multiscale pockets) simultaneously, using several different sizes of spherical probes (multiscale probes). We implemented our algorithm as a new program, ghecom (grid‐based HECOMi finder). The statistics of calculated pockets for the structural dataset showed that our program had a higher performance of detecting binding pockets, than four other popular pocket‐finding programs proposed previously. The ghecom also calculates the shallowness of binding ligands, Rinaccess (minimum radius of inaccessible spherical probes) that can be obtained from the multiscale molecular volume. We showed that each part of the binding molecule had a bias toward a specific range of shallowness. These findings will be useful for predicting the types of molecules that will be most likely to bind putative binding pockets, as well as the configurations of binding molecules. The program ghecom is available through the Web server (http://biunit.naist.jp/ghecom). Proteins 2010. © 2009 Wiley‐Liss, Inc.
Sprache
Englisch
Identifikatoren
ISSN: 0887-3585
eISSN: 1097-0134
DOI: 10.1002/prot.22639
Titel-ID: cdi_proquest_miscellaneous_734023737
Format
–
Schlagworte
Algorithms
,
binding site
,
Binding Sites
,
Computer Simulation
,
Databases, Protein
,
geometry
,
Ligands
,
mathematical morphology
,
Models, Theoretical
,
Molecular Structure
,
pocket
,
Protein Binding
,
Protein Structure, Tertiary
,
Proteins - chemistry
,
Proteins - metabolism
,
Software
,
Surface Properties
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