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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
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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