Location and basic characterization of channels in molecular structures.
Plugin for MOLE 2.0 contains extended options for channel starting point automatic detection, for filtering of obtained channels to select only the relevant channels and allows estimation of basic physicochemical properties of channels.
SoluProt is a web application for prediction of soluble protein expression in Escherichia coli.
SoluProt is one of the latest additions to the family of solubility predictors based on machine learning. The training set is based on the TargetTrack database, which was carefully filtered to keep only targets expressed in Escherichia coli. The negative and positive samples were balanced and equalized for the protein lengths. The independent validation set is derived from the NESG dataset.
The predictor is in its current version based on random forest regression model and employs 36 sequence-based features, e.g., amino acid content, predicted disorder, alpha-helix and beta-sheet content, sequence identity to PDB and several aggregated physico-chemical properties. SoluProt currently achieves accuracy 58.2%, higher than other comparable tools, and is a subject of further active development.
A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.
Provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.