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LINKS TO PROTEIN TOOLS AND DATABASES

ANALYSIS SUITES

SDSC Biology Workbench
EBI Toolbox

CONTACT PREDICTION

CNB-CSIC
GPCPRED
SCRATCH
Univ of Queensland

DISORDERED REGIONS

DISPROT
GMU database
GlobPlot
SCRATCH

DOMAIN ASSIGNMENT (STRUCTURE BASED)

3Dee
Anatomy
BML Domain Server (expert assignment)
BML Domain Server
CATH
DALI/FSSP
DDBASE
Dial
Domain3D
DomainParser
DOMAK
PDOMAINS
PDP
PUU
SCOP

DOMAIN PREDICTION

Scooby-domain
SCRATCH

FOLD RECOGNITION

123D
3D-PSSM
bioinbgu
FUGUE
Libra I
LIBELLULA
LOOPP
PredictProtein
Sparks2
UCLA/DOE Fold Server
WURST

HOMOLOGY MODELLING

3D-JIGSAW
CPHmodels
ESyPred3D
MODELLER
SDSC1
SWISS-MODEL

MISCELLANEOUS TOOLS AND DATABASES

Amino Acid Chemical and Physical Properties
Enzyme Structure Database
Kyte-Doolittle Hydropathy Plots
MaxSprout (reconstruct protein from C-alpha's)
Molecules To Go
PAM Matrix Generation
Protherm
ProtScale
Statistical Analysis of Protein Sequences
Transeq (DNA to protein translation)
WebLogo (sequence logos)

MOTIFS AND DOMAINS (SEQUENCE BASED)

Blocks
COGs
NCBI CDD
Pfam
PRINTS
ProDom
PROSITE
ProtoMap

MUTANT DATABASES

MutaProt
PMD
PMR

NON-REDUNDANT TRAINING SETS

PDB select
PISCES
uniqueProt

SECONDARY STRUCTURE ASSIGNMENT

DSSP (ftp directory of assignments)
DSSP (server)
DSSPcont
HSSP
PALSSE
PROSS
P_SEA
SSA
SecStr
STRIDE
t4 (Delaunay tessellation based)
Voro3D/VoTAP
XTLsstr

SECONDARY STRUCTURE PREDICTION

EVA
Jpred
JUFO mlrprdsec
NPS@
PHD/Predict Protein
PORTER
PREDATOR
PROF
PSIPRED
SABLE
SCRATCH
SOV

SEQUENCE DATABASES

NCBI protein sequence
Swiss-Prot

STRUCTURE CLASSIFICATION

CATH
DALI
FSSP
SCOP

STRUCTURE COMPARISON/ALIGNMENT (PAIRWISE)

Combinatorial Extension
Compound Likeness
DALI
DaliLite
FAST
FATCAT
K2
LGA
MAMMOTH
MATRAS
MINAREA
MultiProt
ProSup
Protein3d
Protein3Dfit
SARF2
SCALI
SCMBB
SSAP
SSM
SuperPose
TOPOFIT
TOPS
VAST
URMS

STRUCTURE COMPARISON/ALIGNMENT (MULTIPLE)

CE-MC
MAMMOTH
MASS
MultiProt
POSA
SSM

STRUCTURE DATABASES

MMDB/NCBI Structure
MSD
OCA
PDB
PDBsum

STRUCTURE DECOYS

CASP predictions
Decoys'R'Us
Free Univ of Brussels
ProStar
Rosetta
Sali comparative model decoys

STRUCTURE VALIDATION

Biotech Validation Suite (PROCHECK, WHAT IF, PROVE)
Delaunay four-body sequence-structure compatibility
PROSA II

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LINKS TO OTHER BIOINFORMATICS TOOLS AND DATABASES

GENE FINDING

GRAIL
GENSCAN
GeneMark

ORGANISM DATABASES

ATCC
TIGR Microbial Genomes

PATHWAYS

Main Metabolic Pathways
Expasy Biochemical Pathways
KEGG
PUMA2

RNA

MFOLD

SEQUENCE ANALYSIS

Dynamic Programming (ALION)
Multiple Sequence Alignment with CLUSTALW
Multiple Sequence Alignment with Match-Box
Translation Machine

SEQUENCE DATABASES

Entrez

Prepared by Todd Taylor; revised 4/14/2006

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