Search Results for "define secondary structure of proteins"

...The similarities may reveal evolutionary history and are clues about common biological functions of the sequences. The information of similarity and difference can then be used to predict the secondary or tertiary structure of new sequences and to find the relationships between sequences. MSA is also often used for constructing evolutionary trees from DNA sequences and for analyzing the structures to help in designing new proteins. Usually, to solve an MSA problem is to find an alignment of multiple sequences with the highest score based on a given scoring criterion among sequences.

...Contact Maps can be used to understand proteins' : 1. Secondary structures 2. Conformational arrangements 3. Surface interactions

SABLE is a public domain package for structural bioinformatics that can be used to predict from amino acid sequence secondary structure and solvent accessibility profiles in proteins (see Adamczak, Porollo and Meller, Proteins 56, 2004).

AlignMe is a C++ program to align distantly related membrane proteins by including several input parameters. Alignments based on substitution matrices, Position Specific Matrices (PSSMs), hydrophobicity scales and any kind of profiles (membrane predictions, secondary structure predictions etc.).

ProteinArchitect facilitates the visual exploration of the architecture of proteins, including conserved domains, secondary structure elements and structurally flexible regions, e.g. in the context of the analysis of protein superfamilies.