What is Expasy used for?
It is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.
What is the pI of my protein?
The isoelectric point (pI) is the pH of a solution at which the net charge of a protein becomes zero. At solution pH that is above the pI, the surface of the protein is predominantly negatively charged, and therefore like-charged molecules will exhibit repulsive forces.
What does the aliphatic index mean?
Aliphatic index. The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins.
How do you calculate protein mass?
If the sequence of amino acids is known for any given protein, we can roughly estimate the molecular weight of the protein by multiplying the average molecular weight of amino acids with the total number of amino acids present in the protein. The average molecular weight of an amino acid is known to be 110 Daltons(Da).
Is pI the same as pH?
The isoelectric point (pI) is the pH of a solution at which the net charge of a protein becomes zero. At solution pH that is above the pI, the surface of the protein is predominantly negatively charged, and therefore like-charged molecules will exhibit repulsive forces.
Why is isoelectric point important?
The isoelectric point is significant in protein purification because it represents the pH where solubility is typically minimal. Here, the protein isoelectric point signifies where mobility in an electro-focusing system is zero—and, in turn, the point where the protein will collect.24-Jul-2012
What does a high aliphatic index mean?
A high aliphatic index indicates that a protein is thermo-stable over a wide temperature range [20]. The GRAVY value for a peptide or protein is calculated as the sum of hydropathy values of all of the amino acids divided by the number of residues in the sequence [17], [21].
What is Boman index?
The Boman Index is an estimate of protein-binding potential, calculated on the basis of cyclohexane-to-water partition coefficient of the respective amino acid side chains divided by the total number of amino acid residues within the peptide [36].
How do you cite a ProtParam tool?
Protein Identification and Analysis Tools on the ExPASy Server; (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005).
What is protein formula?
Protein invariably have the general formula RCH(NH2)COOH, where C is carbon, H is hydrogen, N is nitrogen, O is oxygen, and R is a group, varying in composition and structure, called a side chain.
How do you calculate kDa protein?
Using the equation for the linear plot we can calculate the Log (MW). (-2.0742 x 0.7084) +2.8 = 1.3305. So the inverse log is 10^1.3305= 21.4kDa for the molecular weight of the unknown protein.28-Apr-2014
Is Dalton equal to grams per mole?
Measure of molecular weight or molecular mass. One molecular hydrogen molecular atom has molecular mass of 1 Da, so 1 Da = 1 g/mol.
Protein Sequence Format
The ProteinAnalysis class takes one argument, the protein sequence as a string and builds a sequence object using the Bio.Seq module. This is done just to make sure the sequence is a protein sequence and not anything else.
Available Tools
count_amino_acids: Simply counts the number times an amino acid is repeated in the protein sequence. Returns a dictionary {AminoAcid: Number} and also stores the dictionary in self.amino_acids_content.
Protein Scales
protein_scale (Scale, WindowSize, Edge) : The method returns a list of values which can be plotted to view the change along a protein sequence. You can set several parameters that control the computation of a scale profile, such as the window size and the window edge relative weight value. Many scales exist.