Molecular Weight of DNA

Calculates the molecular weight of a DNA sequence in Dalton.

The weight of a DNA sequence differs depending on if the DNA is assumed to be single or double stranded, circular, or linear and depending on what distribution of isotopes is assumed for the atoms in the DNA.

A monoisotopic DNA sequence is assumed to only contain the most abundant naturally occurring stable isotope for each type of atom.

Input: fasta file

Output: molecular weight

Protein Stability

The protein instability index is calculated based upon the observed frequency of dipeptides in different stable/ unstable proteins and is a heuristic for the stability of protein sequences given the observed differences in dipeptide frequency between stable and unstable proteins.

This Node computes the protein instability index. Values > 40 indicate short half-life of the protein.

Input: fasta file

Output: protein instability index

• Guruprasad, K., Reddy, B. B., & Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, Design and Selection, 4(2), 155-161. DOI: 10.1093/protein/4.2.155

GC Content

This node calculates the ratio of bases guanine (G) and cytosine (C) out of all four possible bases (adenine, guanine, cytosine, thymine (or uracil in RNA)) in a given DNA sequence.

GC content of a sequence can be important to know for the planning of sequencing experiments, PCR reactions and many other experiments that might be sensitive to DNA with an increased melting temperature, as the bases G and C increase a nucleotide’s melting temperature.

Input: fasta file

Output: GC content percentage

Protein Ligand Binding Affinity

The binding affinity of a protein and a ligand is a measure for how well a given protein structure can bind a ligand. This can be important to judge how well a ligand is able to bind into a structure, for example to find the most potent inhibitor of an enzyme.

This node predicts the binding affinity of a given protein structure with a docked ligand.

The binding affinity is predicted in Kcal/mol by the program PRODIGY-LIG. A more negative value is better.

Input: PDB file with an added small molecule

Output: predicted binding affinity in Kcal/mol