RHYTHM: A Knowledge Based Prediction of Helix-Helix Contacts
Motivation
Membrane proteins play a crucial role for the recognition and binding of modulators and associated proteins. Due to difficulties in overexpression and crystallization, their tertiary structure is often predicted using computational methods [1]. The prediction of solvent-accessible vs. solvent-exposed residues is a useful approach for the low resolution tertiary structure modelling of helical membrane proteins [2].
Starting from a given protein sequence, secondary and tertiary structure information is calculated by RHYTHM within only a few seconds. To account for different packing motifs the program uses various approaches for the prediction of channels and transporters (channels) or other membrane proteins (membrane-coils), respectively [3]. The prediction applies structural information from a growing data base of precalculated packing files and evolutionary information from sequence patterns conserved in a represantative dataset of membrane proteins (pfam-domains).
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