CODE Tips of the Week

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...

.mcr file extension – changes to ‘.txt’ When downloading a macro from Canvas, Dropbox, OSF, or other cloud-based sources, sometimes the file extension (.mcr) gets changed to .txt. This is especially common with MacOS users. Alternatively, the extension gets modified...

Database Commons – a catalog of 5860+ worldwide biological databases https://ngdc.cncb.ac.cn/databasecommons/  

https://varsome.com/ Varsome is a database that provides information about genetic variations and their relationships to human health. It is a resource for researchers, clinicians, and other professionals who are interested in understanding the role of genetic...

http://missense3d.bc.ic.ac.uk/ Missense3D predicts the structural changes introduced by an amino acid substitution. It is applicable for the analysis of both PDB (experimental) coordinates and homology-predicted structures. http://missense3d.bc.ic.ac.uk/missense3d/...

https://www.reading.ac.uk/bioinf/IntFOLD/IntFOLD6_form.html IntFOLD from the University of Reading allows you to predict tertiary structures, assess the quality of 3D models, detect disordered regions, predict the boundaries for structural domains and predict likely...

Go to the I-TASSER website (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) and paste your protein’s FASTA sequence into the text box. The maximum number of amino acids that can be inputted in a single job is 1500. If necessary, you can split your FASTA sequence into...

This resource will be valuable if you are interested in the genetics of a particular disease or gene/family of genes. Clinvar (https://www.ncbi.nlm.nih.gov/clinvar/) is a comprehensive list of known genetic variants. These variants are classified as either damaging,...

The ConSurf server (http://consurf.tau.ac.il/2016/) is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences. The degree to...

Link:  https://consurf.tau.ac.il/ Overview: https://consurf.tau.ac.il/overview.php The ConSurf server (Glaser et al., 2003; Landau et al., 2005; Ashkenazy et al., 2010; Celniker et al., 2013; Ashkenazy et al., 2016) is a bioinformatics tool for estimating the...