Protein properties

OBRC

	AACompIdent -- Protein identification tool
	Identify a protein from its amino acid composition.

	AAindex -- Amino Acid index database
	Search for information on property and similarity of amino acids expressed as numerical values.

	BioBayesNet -- a web server for feature extraction and Bayesian network modeling of biological sequence data
	Model and classify biological data using Bayesian networks

	CyBase -- a database of cyclic protein sequences and structures, with applications in protein discovery and engineering
	Search for curated sequence and structure information on cyclic proteins.

	DeNovoID -- a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
	Use degenerate amino acid sequence and mass data derived from mass spectroscopy experiments to search a peptide database.

	EXPASY Proteome Tools Collection
	Use a collection of tools for protein analyses.

	GLUE-IT -- GLUE-Including Translation
	Estimate amino acid diversity in libraries with up to 6 variable codons.

	H++ -- a server for estimating pKas and adding missing hydrogens to macromolecules
	Automatically predict protonation equilibrium pK constants of macromolecules based upon their atomic resolution Protein Data Bank (PDB) structures.

	LINKER -- A web server to generate peptide sequences with extended conformation
	Design linker sequences for constructing functional fusion proteins.

	MPSQ -- Multi-Protein States Query
	A web tool for protein state searching.

	MinActionPath -- maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
	Generate the most probable trajectory between two states.

	PBEQ-Solver -- online visualization of electrostatic potential of biomolecules
	Calculates and visualizes the electrostatic potential of your molecule by solving the Poisson-Boltzmann (PB) equation.

	PCE -- web tools to compute protein continuum electrostatics
	Perform protein electrostatic computations.

	PEDEL-AA -- Programme for Estimating Diversity in Error-prone PCR Libraries
	Estimate the number of distinct protein variants encoded by an error-prone PCR library.

	PFIA -- Peptide Fragment Ion Analyser
	A tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides.

	PHEPS -- web-based pH-dependent Protein Electrostatics Server
	Conduct pH-dependent fast electrostatic analysis.

	PINT -- Protein�protein Interactions Thermodynamic Database
	Search for comprehensive information on protein-protein interaction thermodynamics.

	PPD v1.0 � an integrated, web-accessible database of experimentally determined protein pKa values
	Search for information on protein ionization constants.

	PROFEAT -- a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
	Compute commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence.

	Pepinfo/Pepwindow/Pepstats
	Find amino acid composition and Kyte & Doolittle hydropathy plot for an amino acid sequence.

	ProNIT -- A database for protein�nucleic acid interactions
	Search for information on protein-nucleic acid interactions.

	ProSight PTM -- improved protein identification and characterization for top down mass spectrometry
	Identify and characterize proteins using mass spectra data from �top-down� fragmentation of intact protein ions (i.e. without any tryptic digestion).

	ProTherm -- Thermodynamics Database for Proteins and Mutants
	Search for thermodynamics information on wild type and mutant proteins.

	ProtScale -- amino acid scale computation tool
	Find the physico-chemical properties ( molecular wt, polarity, hydrophobicity, etc.) of an amino acid sequence by selecting appropriate tools.

	Qgrid -- Clustering Tool for Detecting Charged and Hydrophobic Regions in Proteins
	Quickly locate charged and hydrophobic clusters in proteins.

	SAPS -- Statistical Analysis tool of Protein Sequences
	Evaluate protein sequences by statistical criteria.

	Selecton -- Server for the Identification of Site-Specific Positive Selection & Purifying Selection
	Detect positive and purifying selection using a Bayesian inference approach.

	TECRdb -- Thermodynamics of enzyme-catalyzed reactions
	Search for thermodynamic data on enzyme-catalyzed reactions.

	TRITON -- a graphical tool for ligand-binding protein engineering
	Software for protein engineering.

	The FoldX web server -- an online force field
	Conduct rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids.

	The REFOLD database -- a tool for the optimization of protein expression and refolding
	Search for published methods employed in the refolding of recombinant proteins.

	pKD -- re-designing protein pKa values
	Predict changes of protein pKa value due to point mutations.