Protein Sequence Database
Entrez @NCBI (New Entrez)
PIR
(Protein Infomation Resource)a comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available
SWISS-PROT+TREMBL (Another Server)
Protein Structure Database
CATH (Protein structure classification dataabse)
Entrez @NCBI
(New Entrez)
HSSP
NRL-3D
(Sequence structure database)The database is produced by PIR from sequence and annotation information extracted from the PDB of crystallographic structures.
PDB
The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography & NMR.
PROSITE
@ExPASy <Mirror site @Taiwan>
SCOP Structure Classification of Protein
Protein Secondary Structure Prediction
COILS (Lupas-algorithm) Prediction of coiled coil regions in proteins
Multicoil Prediction of two- and three-stranded coiled coils
nnPredict
Paircoil
Prediction of coiled coil regions in proteins (Berger's method)
PHDsec (@PredictProtein) Prediction of transmembrane helix location and topology
PREDATOR
Protein secondary structure prediction from single or multiple sequences
PSA @BioMolecular Engineering Research Center(BMERC)
PSSP / NNSSP @BCM
PSSP / SSP @BCM
SAPS Statistical analysis of protein sequences
SOPM Protein secondary structure prediction
SOPMA Protein secondary structure prediction
Protein Tertiary Structure Prediction
SWISS_MODEL An automated knowledge-based protein modelling server
CPHmodels Automated neural-network based protein modelling server
3D-PSSM Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information ie.Foldfit
SWEET Constructing 3D models of saccharids from their sequences
Swiss-PdbViewer
A program to display, analyse and superimpose protein 3D structures
Homology Modeling
SWISS-Model
Threading Algorithms and Fold Recognition
123D a program which combines substitution matrix, secondary structure prediction, and contact capacity potentials to thread a sequence
throught the set of structures
frsvr @UCLA
ProFIT
THREADER2 (Software download)
TOPITS
Protein Function Prediction
Calculating Hydrophobicity Profiles
Drawchca
Draw an Hydrophobic Cluster Analysis plot of a protein sequence
Plot the Hydropathic Profile of a Protein
PortScale @ExPASy Amino acid scale representation
Predicting Transmembrane Helices
PHDhtm (@PredictProtein)
SOUSI
Prediction of transmembrane regions
TMAP
Transmembrane detection based on multiple sequence alignment
TMpred Prediction of transmembrane regions and protein orientation
Leader Sequences and Protein Localization
PSORT Prediction of protein sorting signals and localization sites
SignalP Prediction of signal peptide cleavage sites
Comparing a Protein Sequence against Motif and Profile Database
BLOCKS Query sequence comparison against the BLOCKS database of
highly conserved regions of protein
MoST Software for Unix
MOTIF
Searching Protein and Nucleic Acid Sequence Motifs @GenomeNet, Japan
MPsrch (Email result)
PatScan a pattern matcher which searches protein or nucleotide
(DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.
PatternFinder Pattern search of SwissProt and GenPept databases @ISREC
Pfam
Protein families database of alignments and HMMs, a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains
Pratt2.1 Pattern discovery tool @Pasteur Inst.
PRINTS database A compendium of protein fingerprints. (Fingerprint is a group of conserved motifs used to characterise a protein family)
PROBE
Software for PC
ProDom database
ProfileScan
Compare a sequence against PROSITE Motifs Database @ISREC
PROSITE
@ExPASy <
Mirror site @Taiwan>
Protein Science Utilities
PIR-ALN (curated database of protein seq. alignments derived from
sequences and annotation in the PIR Database.)
RESID @PIR (database of amino acids modification)
Compute pI/Mw tool Compute the Theoretical pI and Molecular Weight of a Protein Sequence @ExPASy
MHC Peptide Binding Prediction
HLA Bind Prediction of MHC type I (HLA) peptide binding
SYFPEITHI Prediction of MHC type I and II peptide binding
@SYFPEITHI
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