UNIVERSI
TÄ
TS-
BIBLIOTHEK
P
ADERBORN
Anmelden
Menü
Menü
Start
Hilfe
Blog
Weitere Dienste
Neuerwerbungslisten
Fachsystematik Bücher
Erwerbungsvorschlag
Bestellung aus dem Magazin
Fernleihe
Einstellungen
Sprache
Deutsch
Deutsch
Englisch
Farbschema
Hell
Dunkel
Automatisch
Sie befinden Sich nicht im Netzwerk der Universität Paderborn. Der Zugriff auf elektronische Ressourcen ist
gegebenenfalls
nur via VPN oder Shibboleth (DFN-AAI) möglich.
mehr Informationen...
Universitätsbibliothek
Katalog
Suche
Details
Zur Ergebnisliste
Datensatz exportieren als...
BibTeX
A simple and fuzzy method to align and compare druggable ligand-binding sites
Proteins, structure, function, and bioinformatics, 2008-06, Vol.71 (4), p.1755-1778
Schalon, Claire
Surgand, Jean-Sébastien
Kellenberger, Esther
Rognan, Didier
2008
Volltextzugriff (PDF)
Details
Autor(en) / Beteiligte
Schalon, Claire
Surgand, Jean-Sébastien
Kellenberger, Esther
Rognan, Didier
Titel
A simple and fuzzy method to align and compare druggable ligand-binding sites
Ist Teil von
Proteins, structure, function, and bioinformatics, 2008-06, Vol.71 (4), p.1755-1778
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2008
Quelle
Wiley Online Library Journals Frontfile Complete
Beschreibungen/Notizen
A novel method to measure distances between druggable protein cavities is presented. Starting from user‐defined ligand binding sites, eight topological and physicochemical properties are projected from cavity‐lining protein residues to an 80 triangle‐discretised sphere placed at the centre of the binding site, thus defining a cavity fingerprint. Representing binding site properties onto a discretised sphere presents many advantages: (i) a normalised distance between binding sites of different sizes may be easily derived by summing up the normalised differences between the 8 computed descriptors; (ii) a structural alignment of two proteins is simply done by systematically rotating/translating one mobile sphere around one immobile reference; (iii) a certain degree of fuzziness in the comparison is reached by projecting global amino acid properties (e.g., charge, size, functional groups count, distance to the site centre) independently of local rotameric/tautomeric states of cavity‐lining residues. The method was implemented in a new program (SiteAlign) and tested in a number of various scenarios: measuring the distance between 376 related active site pairs, computing the cross‐similarity of members of a protein family, predicting the targets of ligands with various promiscuity levels. The proposed method is robust enough to detect local similarity among active sites of different sizes, to discriminate between protein subfamilies and to recover the known targets of promiscuous ligands by virtual screening. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Sprache
Englisch
Identifikatoren
ISSN: 0887-3585
eISSN: 1097-0134
DOI: 10.1002/prot.21858
Titel-ID: cdi_hal_primary_oai_HAL_hal_00620777v1
Format
–
Schlagworte
Algorithms
,
alignment
,
Amino Acid Sequence
,
binding site
,
Binding Sites
,
Binding Sites - drug effects
,
chemogenomics
,
Drug Design
,
Hydrogen Bonding
,
Life Sciences
,
ligand
,
Ligands
,
Pharmaceutical sciences
,
Protein Binding
,
Sequence Alignment
,
similarity
,
Structure-Activity Relationship
Weiterführende Literatur
Empfehlungen zum selben Thema automatisch vorgeschlagen von
bX