CODE Tips of the Week

CODE Tip – gnomAD – Healthy Individual Variant Database

The Genome Aggregation Database (gnomAD) (http://gnomad.broadinstitute.org/) is a collection of roughly 125,700 exomes and 15,700 whole genomes. This reference population database can be an essential tool in variant and gene interpretation, allowing you to distinguish...

CODE Tip MobiDB Protein Structural Dysfunction Prediction

Are you interested in why a protein may not have any homology, resulting in no known structures in the Protein Data Bank? You can utilize http://mobidb.bio.unipd.it to determine which portions, if any, are of known structure. MobiDB analyzes a protein structure and...

CODE Tip YASARA File Types

There are three (3) different file types associated with YASARA. Each one of these serves its own purpose. .pdb file: The “protein-databank file” or pdb is a general-purpose file that can be opened in many different protein-viewer software. This file type maintains...

CODE Tip NCBI – Conserved Domain Database

https://www.ncbi.nlm.nih.gov/cdd/?term= Conserved domains are recurring units in molecular evolution and appear in protein sequences as conserved blocks of amino acid residues that have distinct functions. Conserved domains serve as building blocks and can be...

CODE Tip – Residual Variation Intolerance Score (RVIS)

An RVIS score is a tool for measuring genetic mutation intolerance. The tool ranks protein-coding genes based on their intolerance to functional variation by comparing the overall number of observed variants in a gene to the observed common functional variants. RVIS...

CODE Tip of the Week (Tip #21)

Tip #21 This week’s tip will introduce a new tool which predicts possible impact of amino acid substitutions on the structure & function of proteins. PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/dokuwiki/start) is a pathogenicity prediction tool that...

CODE Tip of the Week (Tip #20)

Tip #20 I recently stumbled across a tool that could be of high utility. This tool is ClinvarMiner (https://clinvarminer.genetics.utah.edu/). ClinvarMiner allows you to search by gene, disease, or submitter and provides a comprehensive list of all variants submitted...

CODE Tip of the Week (Tip #1)

Tip #1 : What do you do if your protein does not model in YASARA, or if only a portion of it will model? You can model the remaining portion of the protein with the I-TASSER website (https://zhanglab.ccmb.med.umich.edu/I-TASSER/). Paste your desired FASTA...

CODE Tip – gnomAD – Healthy Individual Variant Database

CODE Tip MobiDB Protein Structural Dysfunction Prediction

CODE Tip YASARA File Types

CODE Tip NCBI – Conserved Domain Database

CODE Tip – Residual Variation Intolerance Score (RVIS)

CODE Tip of the Week (Tip #21)

CODE Tip of the Week (Tip #20)

CODE Tip of the Week (Tip #1)

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