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Taiwan Bioinformatics Institute

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Tools/Databases for Structural Biology

Protein three-dimensional structure is crucial to its function. The prediction of protein structure is thus a very important task in the post-genomic era. Structure prediction of a novel sequence involves gene prediction and gene annotation. Multiple sequence alignment is conducted as a way to find clues from known protein motif/domain in the databases, and molecular modeling techniques are then used to predict 3D structure from sequence information. When functional domain has been identified and defined, molecular docking techniques can be used to determine functional structure unit of protein binding and is a very powerful tool for drug design. The following are links to various databases and tools in the above mentioned areas that are helpful in structure analysis.

Gene Prediction, Gene Annotation

dbPTM
 
Gene Prediction
 
GPDB
 
miRNAMAP
 
ProSplicer
 
RegRNA
 
RNAMST
 
SCEPTRANS
 
YRC
 
     

Sequence Alignment

PDB-BLAST
 
ClustalW
 
MuSiC
 
     

Protein Domain/Motif Search

ASEdb
 
CELLO
 
     

Protein Structure Search

CATH
 
PDB
 
pKNOT
 
prokware
 
     

Protein Structure Dynamic

oGNM
 
     

Molecular Modeling

(PS)2
 
PredictProtein
 
SWISS-MODEL
 
     

Docking and Drug Design

AutoDock
 
GEMDOCK
 
GRAMM-X
 
PatchDock
 
     

Structural Comparison & Classification

3D-BLAST
 
CE
 
CPSARST
 
SARST
 
SCOP