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 residues, as well as from the previously constructed...
Multicoil2 significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coiled-coil sequences. The new database, comprised of 2,105 sequences containing 124,088 residues, includes reliable...
Sequence analysis Paircoil2:improved prediction of coiled coils from sequence A.V.McDonnell1,T.Jiang2,†,A.E.Keating2,Ãand B.Berger1,Ã 1Mathematics Department,Computer Science and Artificial Intelligence Laboratory and2Department of Biology, Massachusetts Institute of Technology,Cambridge,MA...
Recent advances in machine learning-based protein structure prediction20 and generative protein design21,22,23,24 opened tremendous potentials for engineering biological systems, by generation of new scaffolds and protein binders that enable the design of new protein functions. However, smaller protein mo...
Meanwhile, the rules that can explicitly explain the prediction results of the test coiled coil can be extracted from the AAFreqCoil model for a better explanation of user predictions. A web server and stand-alone program implementing the AAFreqCoil algorithm are freely available athttp://...
To test the prediction that Q/N-rich and polyQ stretches can be part of α-helical CC structures, and to assess effects of the CC mutations, we used circular dichroism (CD) to analyze the secondary structure of three sets of peptides (Figure 4A). CD is used extensively to study the fo...
paircoil2 improved prediction of coiled coils from sequence 热度: de novo predictions of the quaternary structure of leucine zippers and other coiled coils 热度: Policy divergence and voter polarization in a structural model… 热度: 相关推荐 JournalofStructuralBiology154(2006)111–121 .elsevier...
Our result shows 73\\% accuracy on the prediction of anti-parallel coiled coils based on the cross-validated data. The result suggests a useful approach of using SVM to classify the anti-parallel coiled coils based on the primary amino acid sequence....
G., Prediction of the stability of coiled coils using molecular dynamics simulations. Molecular Simulation 2007,33 (6-8), 463-473. 52. Religa, T. L, Comparison of multiple crystal structures with NMR data for engrailed homeodomain. Journal of Biomolecular NMR 2008,40 (3), 189-202....
A "web version":http://www.bioinf.jku.at/software/procoil/ and an "R package":http://www.bioinf.jku.at/software/procoil/procoilR.html of our prediction and profiling software (PrOCoil) are available to the scientific community.doi:10.1038/npre.2010.4677.1Carsten C Mahrenholz...