Questions tagged [computational-biochemistry]
The computational-biochemistry tag has no usage guidance.
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What is the Manchester style encoding of gene-protein associations
From SBML Level 3 Package: Flux Balance Constraints (`fbc'), page 11
A GeneProduct may, optionally, refer to a Species so as to provide compatibility with the Manchester style encoding of gene-...
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SHAP correlation patterns for model prediction of protein are confusing
I have developed an ANN model to predict protein post-translational modification patterns from Elisa data. For simplicities sake, the how, feasibility and parameters aren't important for my question ...
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What is the difference between flat and stereo stitch id?
For my thesis, I'm working on side effect prediction in a machine learning framework and I am working on data available on SIDER (http://sideeffects.embl.de/download/). If you open the README file, ...
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Converting miRNA names to miRBase version IDs
I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example:
hsa-miR-106a ---> hsa-miR-106a-5p
hsa-miR-373* --> hsa-miR-373-5p
hsa-miR-33 --> hsa-miR-33a-5p
...
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Best reference book for basic concepts when working with bioinformatics
I'm starting to study Bioinformatics, I already have basic knowledge of Biochemistry and Genetics, but I want to buy a reference book, to use when I forget a concept (I'm a Computer Science student, ...
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Which components must be included in the HDR plasmid?
I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues.
I wanted to know exactly which components must be included in the plasmid.
I know that I have ...
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Question about Using MDAPackmol (packmol in python)
I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on GitHub so I can gain an ...
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Seeking Advice on Acquiring Clean Experimental data comprises of proteins for FDR Estimation
I am a bioinformatics student doing my research on top-down mass spectrometry-based proteomics and seeking some guidance on acquiring very clean experimental data with known true positives and false ...
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Issues with AutoDock Vina
I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
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