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Bioinformatics
Databases / Servers
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Structure Databases: PDB,
PDBsum, SCOP,
FSSP,
CSA,
Dock Ground
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Ligand Databases: ZINC, Super Drug, PRECISE, KEGG
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HIV Databases: Stanford, LANL,
NIST
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Docking Servers: ClusPro, ZDOCK,
SmoothDock, RosettaDock, GRAMM-X, PatchDock
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Sequence Analysis: BLAST,
EBI collection
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Structure Alignment: DALI, CE,
TM-Align
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Homology Modeling /
Protein Structure Prediction:
SWISS-MODEL (~min, multi or specified template), M4T (~min, multi),
LOMETS (~hr, meta server), I-TASSER (~d, accurate), QUARK (~d, ab
initio + knowledge, accurate) RaptorX
(~d, works for remote or low homology, w/ ab initio, accurate), Robetta (~w, great ab initio
when template is missing, accurate)
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