We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices) of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the
We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices) of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the previous Multicoil method with the flexibility of Hidden Markov Models (HMMs) in a ...
. The main reason for this wide gap is unavailability of protein structure, which is used to assign the structural class, for the significant majority of the known protein sequences. To this end, an accurate and automated method for classification of sequences into the corresponding structural cl...
Large number of proteins chains that are of interest to the biologists (which are being deposited to PDB) and that share twilight-zone pairwise identity with the chains for which the structure is known, and the potential structural similarities between these protein sequences that can be exploited...
At pres- ent, the developing directions of IDP prediction include three aspects as follows: (1) Improve the accuracy of the prediction for IDPs, especially short disordered regions and disorder in N- and C-terminal regions of protein sequences. In the prediction process, these regions are ...
In the method of the present invention, a model for the folded structure of a set of proteins is built from a set of aligned homologous protein sequences. The method of the present invention is characterized by several operational features, each of which is essential for the method to be ...
ILP has been successfully applied to a variety of learning problems, such as predicting sequence-based homology and gene/protein function [25], finding regularities in microarray data [26], modeling protein–ligand [27] and protein–protein interactions [28], discovering pharmacophores [29], and ...
Due to their ability to oligomerize, coiled coils are involved in a variety of important cellular functions, either on their own or as part of larger protein complexes. Hence, they are in the focus of current research, for instance, as potential oncogenes and in the context of viral fusion...
Analysis of the MultiCoil scores provides insight into structural features of coiled coils, and yields estimates that 0.9% of all protein residues form three-stranded coiled coils and that 1.5% form two-stranded coiled coils. The MultiCoil program is available at http://theory.Ics.mit.edu/...