MARCOIL

[…] bayesian posterior probabilities (10,000,000 generations)., the ncbi cd-search was used to identify conserved domains. secondary structure elements and folds were predicted in phyre2 (). pcoils and marcoil (http://toolkit.tuebingen.mpg.de) were used for prediction of coiled-coil regions and the presence of heptad repeats., phytophthora p. infestans rna was kindly provided by sebastian […]

[…] used to predict the molecular changes associated with amino acid variants []. it uses sift, psi-blast, and pfam profiles along with some structural disorder prediction algorithms, including tmhmm, marcoil, i-mutant 2.0, b-factor prediction, and disprot []. functional analysis includes the prediction of dna-binding site, catalytic domains, calmodulin-binding targets, and posttranslational […]

[…] hsf proteins were defined by merging the results from the pfam (http://pfam.xfam.org/), the heatster (http://www.cibiv.at/services/hsf/), the smart (http://smart.embl-heidelberg.de/), and the marcoil (http://toolkit.tuebingen.mpg.de/marcoil) programs. the aha, nuclear localization signal (nls), nuclear export signal (nes) and rd structures were detected based on the heatster […]

[…] long. sequence analyses were performed in the mpi bioinformatics toolkit (alva et al., ; https://toolkit.tuebingen.mpg.de) using quick2d, hhpred (hildebrand et al., ), pcoils (lupas et al., ), and marcoil (delorenzi and speed, ). transmembrane segments were predicted with fmhmm (sonnhammer et al., ) and phobius (käll et al., ). for transcriptional fusions, comparisons between samples […]

[…] with coiled‐coil interacting regions(maestro et al., ; mezzina and pettinari, ). this common structure suggests that the mode of oligomerization could be determined by the coiled‐coil regions. using marcoil (delorenzi and speed, ; mezzina et al., ), phapaz was found to have a maximum probability of 32% of coiled‐coil regions for homo‐oligomerization, while phaptd contains a high coiled‐coil […]

[…] cc motifs , . we have used these signature sequences to classify the non-tnl family. the presence of cc regions was further validated by hmmer search (phmmer) against uniprotkb protein database and marcoil server using 9fam matrix. the probability of n-terminal region showing coiled coil conformation in the marcoil plot was in the range of 0.4-1 for most of the non-tnl proteins., the canonical […]

[…] data strongly suggested that the heptad repeat and, therefore, most likely a coiled-coil motif in this n-terminal portion of the protein likely played a role in inducing the mt effects., using the marcoil coiled-coil prediction algorithm (, ) to analyze the primary rrv orf52 sequence, we noted that the polypeptide encompassing residues 14 to 39 and containing the heptad repeats had a 50 to 97% […]