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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
Sequence Alignment
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PDB-BLAST
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http://ibm5.life.nthu.edu.tw/XCC_HP/blast_new/blast/blast_pdb.html | |
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ClustalW
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http://biobug.life.nthu.edu.tw/clustalw/ | |
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MuSiC
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http://genome.life.nctu.edu.tw/MUSIC/ | |
Protein Domain/Motif Search
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ASEdb
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http://nic.ucsf.edu/asedb/ | |
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CELLO
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http://cello.life.nctu.edu.tw/ | |
Protein Structure Search
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CATH
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http://www.cathdb.info/index.html | |
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PDB
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http://pdb.life.nthu.edu.tw/ | |
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pKNOT
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http://pknot.life.nctu.edu.tw/ | |
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prokware
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http://prokware.mbc.nctu.edu.tw/ | |
Protein Structure Dynamic
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oGNM
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http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm | |
Molecular Modeling
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(PS)2
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http://ps2.life.nctu.edu.tw/ | |
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PredictProtein
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http://biobug.life.nthu.edu.tw/predictprotein/ | |
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SWISS-MODEL
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http://swissmodel.expasy.org//SWISS-MODEL.html | |
Docking and Drug Design
Structural Comparison & Classification
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3D-BLAST
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http://3d-blast.life.nctu.edu.tw/ | |
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CE
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http://cl.sdsc.edu/ | |
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CPSARST
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http://sarst.life.nthu.edu.tw/cpsarst/ | |
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SARST
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http://sarst.life.nthu.edu.tw/sarst/ | |
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SCOP
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http://scop.life.nthu.edu.tw/ | |
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