Learning

Bioinformatics research is a journey of learning and the only way to make progress is to patiently explore. The tutorials for YASARA modeling software program and other online tools provided here will help you make that progress. Once you are familiar with a bioinformatic tool, search through the Protocols for specific tasks you want to accomplish. The CODE Tips of the Week will provide short and helpful information that you might not have discovered yet. Check out the VUS List for genomic variants of uncertain significance that have been identified in patients –a great place to start a research project!

Tutorials And Protocols

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Analysis of Molecular Dynamics Simulations

Analysis of Molecular Dynamics Simulations

Upon completion of MDS you will find the analysis files generated under the 800 sim files. There will be two files of data titled analysis.tab & analysisRes.tab. Analysis.tab uses root-mean square deviation to track the global movement of the carbon-alpha...

Merging multiple portions of a protein inside of YASARA

Merging multiple portions of a protein inside of YASARA

This protocol will describe the steps to connect two pieces of a protein model together.  You may have a portion of the protein created by homology modeling in YASARA and an additional portion created by threading with I-TASSER, or maybe two portions of the model from...

Running Molecular Dynamic Simulations Inside of YASARA

Running Molecular Dynamic Simulations Inside of YASARA

Molecular dynamics is a simulation methodology often used for studying the conformational rearrangements of molecules and their interactions with other molecular species in a range of environments. Potential applications include variant analysis, ligand docking, and...

Information and Tips

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CODE Tip of the Week (Tip #2)

The first question that comes up whenever you find a gene or disease of interest should be "Does a model of the protein structure already exist?" The way to determine this is by utilizing the public server that everyone was given access to during the workshop. By...

Documents

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CODE VUS List

CODE VUS List

Please use this Google Drive link to find VUS' of interest, as well as keeping a log of who is working on what.   https://docs.google.com/spreadsheets/u/3/d/1sxfH8qXaQP6wjxOeJqh7cVDrH82oY3Z2Rtw6le4J6JA/edit?usp=drive_web&ouid=116014196853061230255

Variant Descriptions and Consequences

Variant Descriptions and Consequences

The table attached below is from Ensembl and provides a description of each variant type from the Sequence Ontology database. The IMPACT rating is described on this Ensemble Glossary page. Variant Descriptions and Consequences (Please Click to Download PDF)

Slide Decks

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