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.
Allows protein sequence analysis. ANTHEPROT is able to interactively couple multiple alignments with secondary structure predictions. It can submit tasks on a remote server and retrieve data from a remote Web server. This tool is a complete solution for Intranet protein sequence analysis for universities, biological research institutes or biomedical companies. It permits users to integrate secondary structure predictions within multiple alignment and full interactive editing of alignments.
Provides access to a variety of public and in-house bioinformatics tools. The MPI Bioinformatics Toolkit integrates a selected set of most useful methods for the analysis of protein sequences and structures. It offers more of 50 interconnected tools, so that the results of one tool can be forwarded to other tools. It also includes a useful platform for teaching bioinformatic enquiry to students in the life sciences.
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.
Performs calculation of the basic property of peptides/proteins, including the isoelectric point (pI), hydrophobicity (Hy) and mass weight (MW). ProPAS allows analysis of the data in local computer, which can be used to process small or large-scale datasets. The software provides the statistic results to get the protein/peptide number distribution of these physicochemical properties.
Allows computation of properties of protein sequences. PHYSICO is an automated standalone, multipurpose procedure for analysis of protein sequences. The software acts as position-based-substitution (PWS) analyzer as 3-in-1 form. It provides users flexibility for input-parameters and helps auto-preparation of BLOCKFASTA file.
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.
Computes more than 50 structure-based features for any given protein structure. PDBparam can deal with inter residue interactions, amino acid propensities, physicochemical properties, and binding sites. It allows to understand the structure and functions of proteins and their complexes. The tool provides deep insights into its structure-function relationship. It can be used for largescale analysis of different types of proteins to explore potential interactions and contacts.
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.
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.
0 - 0 of 0
1 - 3 of 3
Filters / Sort by
0 - 0 of 0