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CCBuilder
Tackles the problem for a defined but large class of protein structure, the alpha-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface (GUI) provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly.
COILCHECK
Allows users to identify and compare weak and strong regions within coiled-coil structures. COILCHECK contains functions for hydrogen atom fixing and hydrogen bond energy calculation to accurately describe the prevailing stabilizing interaction at coiled-coil interface. It offers users to choose distant-dependent dielectric constant in electrostatic energy calculation. This tool includes a structural analysis algorithm called CHAHO in order to study the presence of charged residue patches and ‘hydrophobic ladder’.
Multicoil
Predicts both the location and oligomerization state (two versus three helices) of coiled coils in protein sequences. Multicoil2 uses the flexibility of hidden Markov models (HMMs) in a Markov random field (MRF). The resulting algorithm integrates sequence features, including pairwise interactions, through multinomial logistic regression to devise an optimized scoring function for distinguishing dimer, trimer and non-coiled-coil oligomerization states; this scoring function is used to produce Markov random field potentials that incorporate pairwise correlations localized in sequence.
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