Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Explores the interactions of helical peptides of up to 50 residues with membranes of various types. MCPep is a server designed for non-experts wishing to perform Monte Carlo (MC) simulations of helical peptides in association with lipid membranes. The software simulates the peptide in the aqueous phase and membrane environments, both described implicitly. It reports the main determinants of peptide-membrane interactions, e.g. average location and orientation in the membrane, free energy of membrane association and the peptide's helical content.
Predicts peptide-bilayer binding geometries. 3D-HM extends the idea of molecular hydrophobicity potentials (MHPs), which are based on heuristic or experimental definitions of hydrophobicity for whole residues, molecular fragments, or individual atoms. It is applicable to arbitrary molecular structures, not only to regular conformations like alpha-helices or beta-sheets. This tool performs molecular dynamics (MD) simulations to calculate the hydrophobic moment (HM) time average over a realistic ensemble of highly dynamical peptide structures in fluid membranes.
Offers a platform for determining the length of the hydrophobic region in membrane proteins. MEMHlength first orients the protein structure for performing a hydrophobic length calculation. The application returns an oriented structure and the computed length accompanied by the inward and outward residues. Users can set some options relative to the file orientation and the implicit model.
Provides a useful screening operation for identifying their membrane-based segments. TM Finder is an application that automates and implements the concept of dual threshold hydrophobicity and nonpolar phase helicity requirements to locate protein transmembrane (TM) segments from primary sequences alone. This program also has the power to distinguish essentially unequivocally between membrane and nonmembrane proteins.
Indentifies lipid accessible residues from the protein structure, implemented in the RosettaMP framework and available as a webserver. mp_lipid_acc method uses protein structures transformed in membrane coordinates, for instance from PDBTM (Protein Data Bank of transmembrane proteins) or OPM (Orientations of Proteins in Membranes) databases, and a defined membrane thickness to classify lipid accessibility of residues. mp_lipid_acc is applicable to both a-helical and b-barrel membrane proteins of diverse architectures with or without water-filled pores and uses a concave hull algorithm for classification.
A user-friendly, intelligent membrane analysis tool that automatically interprets a variety of input formats and force fields, is compatible with both single and double bilayers, and capable of handling asymmetric bilayers and lipid flip-flopping. Membrainy has been designed for ease of use, requiring no installation or configuration and minimal user-input to operate.
Graphs the hydrophobicity/hydrophilicity of a sequence of amino acids. Hydrophobicity Grapher provides a sliding window whose size can be specified by the user. Several hydrophobicity scales can be used to determine the plot. Because of how the plot is calculated, the very beginning and very end of the sequence will be cut off. The amount cut off will depend on the window size: exactly one half of the window size will be deleted from the beginning of the sequence, and the same amount will be cut off the end.
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