Superimpose: a 3D structural superposition server.
The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implemented and various databases are provided. Superimposé assists the user regarding the selection of a suitable combination of algorithm and database. After the computation on our server infrastructure, a visual assessment of the results is provided. The structure-based in silico screening for similar drug-like compounds enables the detection of scaffold-hoppers with putatively similar effects. The possibility to find similar binding sites can be of special interest in the functional analysis of proteins. The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimposé server is available at: http://bioinformatics.charite.de/superimpose.
Bauer
Raphael A
RA
Charité-Universitätsmedizin Berlin, Structural Bioinformatics Group, Arnimallee 22, 14195 Berlin, Germany.
Bourne
Philip E
PE
Formella
Arno
A
Frömmel
Cornelius
C
Gille
Christoph
C
Goede
Andrean
A
Guerler
Aysam
A
Hoppe
Andreas
A
Knapp
Ernst-Walter
EW
Pöschel
Thorsten
T
Wittig
Burghardt
B
Ziegler
Valentin
V
Preissner
Robert
R
D000465:Algorithms; D001665:Binding Sites; D016208:Databases, Factual; D020407:Internet; D008958:Models, Molecular; D008968:Molecular Conformation; D004364:Pharmaceutical Preparations / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D012984:Software; D040681:Structural Homology, Protein
D004364:Pharmaceutical Preparations; D011506:Proteins