Multicoil - HMM : improved prediction of coiled - coil oligomer state from sequence
نویسندگان
چکیده
sequence by Jason Trigg S.B. Electrical Engineering and Computer Science, M.I.T., 2010 Submitted to the Department of Electrical Engineering and Computer Science in Partial Fulfillment of the Requirements for the Degree of Master of Engineering in Electrical Engineering and Computer Science at the Massachusetts Institute of Technology MASSACHUSETTS INS TITUTE OF TECHNOL1OGY August, 2010 F @2010 Massachusetts Institute of Technology DEC 162010 All rights reserved. LIBRARIES
منابع مشابه
SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences
MOTIVATION The coiled coil is a ubiquitous α-helical protein structure domain that directs and facilitates protein-protein interactions in a wide variety of biological processes. At the protein-sequence level, coiled coils are quite straightforward and readily recognized via the conspicuous heptad repeats of hydrophobic and polar residues. However, structurally they are more complicated, existi...
متن کاملMulticoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone
The alpha-helical coiled coil can adopt a variety of topologies, among the most common of which are parallel and antiparallel dimers and trimers. 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 flex...
متن کاملMultiCoil: a program for predicting two- and three-stranded coiled coils.
A new multidimensional scoring approach for identifying and distinguishing trimeric and dimeric coiled coils is implemented in the MultiCoil program. The program extends the two-stranded coiled-coil prediction program PairCoil to the identification of three-stranded coiled coils. The computations are based upon data gathered from a three-stranded coiled-coil database comprising 6,319 amino acid...
متن کاملLOGICOIL - multi-state prediction of coiled-coil oligomeric state
MOTIVATION The coiled coil is a ubiquitous α-helical protein-structure domain that directs and facilitates protein-protein interactions in a wide variety of biological processes. At the protein-sequence level, the coiled coil is readily recognized via a conspicuous heptad repeat of hydrophobic and polar residues. However, structurally coiled coils are more complicated, existing in a wide range ...
متن کاملComparative analysis of coiled-coil prediction methods.
In this study we compare commonly used coiled-coil prediction methods against a database derived from proteins of known structure. We find that the two older programs COILS and PairCoil/MultiCoil are significantly outperformed by two recent developments: Marcoil, a program built on hidden Markov models, and PCOILS, a new COILS version that uses profiles as inputs; and to a lesser extent by a Pa...
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