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Full-Text Articles in Life Sciences
Minimotif Miner 3.0: Database Expansion And Significantly Improved Reduction Of False-Positive Predictions From Consensus Sequences., Tian Mi, Jerlin Camilus Merlin, Sandeep Deverasetty, Michael R. Gryk, Travis J. Bill, Andrew W. Brooks, Logan Lee, Viraj Rathnayake, Christian A. Ross, David P. Sargeant, Christy L. Strong, Paula Watts, Sanguthevar Rajasekaran, Martin Schiller
Minimotif Miner 3.0: Database Expansion And Significantly Improved Reduction Of False-Positive Predictions From Consensus Sequences., Tian Mi, Jerlin Camilus Merlin, Sandeep Deverasetty, Michael R. Gryk, Travis J. Bill, Andrew W. Brooks, Logan Lee, Viraj Rathnayake, Christian A. Ross, David P. Sargeant, Christy L. Strong, Paula Watts, Sanguthevar Rajasekaran, Martin Schiller
Life Sciences Faculty Research
Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins …
Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller
Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller
Life Sciences Faculty Research
Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.
A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald
A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald
Dartmouth Scholarship
Molecular replacement (MR) often plays a prominent role in determining initial phase angles for structure determination by X-ray crystallography. In this paper, an efficient quaternion-based algorithm is presented for analyzing peaks from a cross-rotation function in order to identify model orientations consistent with proper non-crystallographic symmetry (NCS) and to generate proper NCS-consistent orientations missing from the list of cross-rotation peaks. The algorithm, CRANS, analyzes the rotation differences between each pair of cross-rotation peaks to identify finite subgroups. Sets of rotation differences satisfying the subgroup axioms correspond to orientations compatible with the correct proper NCS. The CRANS algorithm was first …