Kawabata-lab:Links

Links

LastModified:Sep 30, 2010

Database

DNA Sequence Database
- DDBJ
- NCBI
- EBI
Genome/Gene Database
Protein Sequence Database
Family/Profile database
3D Structure Database
3D Structure Classification
Database for Active/Binding Sites in 3D structures
EM density map Database
- EMsearch : for Electron Microscopy data
- EM Navigator
Other Structural Database
- PDBsum
- PQS : Protein Quaternary Structure database
- Het-PDB Navi : for non-protein molecule in PDB
- LigASite :A gold-standard dataset of biologically relevant binding sites in protein structures
Genomic Sequence Data
Analysis (General)
- COG(Cluster of Orthologous Groups)
- KEGG encycropedia
Ontology
- Gene Ontology Consortium
Assigning 3D structure
Single Nuclotide Polymorphism (SNP)
Metabolic Pathways
Protein-Protein Interaction
Specific Family
- MEROPS the peptidase database
- kinase.com database of protein kinases
Small Compound Database
- Ligand Expo (in RCSB)
- Cambridge Structural Database
- Cambridge Structural Database (Osaka University)
- ZINC
- PubChem
- ChEMBL
- ChEBI
- The Binding Database
- KiBank
- AffinDB
- GLIDA:GPCR-ligand database
- DUD: A Directory of Useful Decoys
- KEG LIGAND
- KEG DRUG
- SUBCOMP Search:Chemical Substructure Search
- SIMCOMP Search:Chemical Similarity Search
- DrugBank : Drug data with drug targets.
- STITCH: interaction networks of chemicals and proteins
- ChemBank High-throughput biological assays from screening projects.
- PDSP NIMH Psychoactive Drug Screening Program

Service / Software

Sequence Homology Search / Sequence Alignment
- BLAST/PSI-BLAST
- FASTA
- EMBOSS
- HMMER
Multiple Sequence Alignment
- ClustalW2
- ClustalW
- ClustalX(ebi)
- ClustalX(u-strasbg)
- T-COFFEE
- MUSCLE
- MAFFT
Gene Finding
- NCBI:gorf
Phylogenetic Analysis
- Phylip
- MEGA
- PAUP
- NJplot
- TreeView
- TreeViewX
Multiple Aligned Sequence Viewer
- JalView
- WebLogo
3D structure prediction (general)
- CASP
Homology Modelling
- FAMS
- SWISS-MODEL
- MODELLER
Fold Recoginition
- GenTHREADER/PSIpred
- FUGUE
- 3D-pssm
- bioinbgu
Ab initio Prediction
- ROBETTA
Secondary Structure Prediction
- PredictProtein
- PSIPRED
Prediction of Intrinsically Disordered region
- PNDR
- DISOPRED
- POODLE
Molecular Graphic Softwares
- RasMol
- Chime
  Chime turorial
- Jmol
- Jmol Script Documentation
- Jmol JavaScript Library
- jV
- MolScript
- Grasp
- CHIMERA
- VMD
- PyMOL
- BALLView
- Swiss PDB Viewer
Global Structure Comparison Servers
- MATRAS
- DALI server
- CE
- VAST
- TOPS
- SAP server
- SAP software download
Local Atomic Structure Comparison Servers
- eF-seek
- GIRAF
Finding Pockets on Protein Surface
- SURFNET
- PASS
- CASTp
- Q-SiteFinder
Molecular Simulation Programs
- Amber
- CHARMM
- TINKER
- NAMD
- GROMACS
Docking Programs(small ligand - protein)
- AutoDock
- AutoDock Vina
- UCSF DOCK
- DOCK Blaster
- GOLD
- myPresto
Docking Programs(protein-protein)
- 3D-Dock Suite (FTDock,RPScore,MultiDock)
- ZDOCK
- MolFit
- PatchDock
- RosettaDock
Tool kit for chemical compound data
- Open Babel
- Chemistry Development Kit (CDK)
- RDKit (Chemoinformatics and Machine Learning Software)
- SMSD(Small Molecular Subgraph Detector)
Chemical structure editor
- BKChem
Electrostatics calculation
- DelPhi
- UHBD
- APBS
Movement/Normal Mode Analysis
- Database of Macromolecular Movements
- UMass Morph Server
- ProMode
Prediction of Phosphorylated sites
- Phospho.ELM
- dbPTM
- NetPhosK
- Scansite
- GPS(Group-based prediction system)
Other Post-translational Modification
- Sulfinator
- SulfoSite
Prediction of Transmembrane Helix
- SOSUI
- TMHMM-2.0
- TMpred
Electron Microscopy
- SITUS
- EMfit
- 3SOM
Other Structure Analysis
- DSSP

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