ShujiaHuang/qmplot Star40 Code Issues Pull requests A Python package for creating high-quality manhattan and Q-Q plots from GWAS results. visualizationpythongwasmatplotlibgwas-toolsgenomics-data-visualization UpdatedDec 27, 2023 Python akcorut/kGWASflow ...
The ability of Java to interact with other software tools is demonstrated by the design of a Ramachandran plot applet that interacts with and controls a virtual reality (VRML) scene of a pair of rotating peptide planes using an External Authoring Interface (EAI)....
show xvg data by scatter plot xvg_show_stack : show xvg data by stack area plot xvg_box_compare : compare xvg data by violin and scatter plots xvg_ave_bar : calculate and show the averages of parallelism xvg_rama : draw ramachandran plot from xvg data XPM: xpm_show : visualize xpm ...
Sachdeva G, Kumar K, Jain P, Ramachandran S (2005) SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks. Bioinformatics 21:483–491 Article PubMed CAS Google Scholar He Y, Xiang Z (2010) Bioinformatics analysis of Brucella vaccines and vaccine...
all of which indicated a high overall quality for the model. The Ramachandran plot showed that 91.7% of the residues were in the most favored regions, with 1.7% of residues in disallowed regions. These disallowed residues are located in loops, which are often poorly defined. These values are...
The tertiary structure model of Malus domestica HMGR (accession number: ABQ52378) was further checked by the PROCHECK algorithm, which showed that 90.3% of the amino acid residues were located in the most favored regions in a Ramachandran plot, indicating that the simulated three-dimensional ...
At the time of writing, wwPDB validation reports for 3DEM structures include: (a) assessment of model geometry similar to that used for all MX and NMR structures (ClashScores, Ramachandran outliers, sidechain outliers, nucleic acid polymer backbone outliers); (b) orthogonal projections of map an...
To evaluate the quality of the cut matrix generated by these tools, CENTIPEDE motif footprinting was performed on the generated cut matrices, and the quality of the motif footprint plot was inspected for differences. Two loci were selected to more specifically compare the cut frequency profile ...
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The results of homology modeling demonstrated that SGD58 have 88.6% of favored regions based on Ramachandran plot. Protein–protein docking with Swarm Dock reveals SGD58 with receptor complex have −54.74 kcal/mol of binding energy with more than 20 interacting residues. Docked complex are stable...