The Protein Science January 2022 Tools issue contains 25 articles highlighting updates and usage of well-loved programs and/or databases to aid research in protein science, as well as several descriptions of new programs. These articles present tools for a number of biochemical and biophysical techniques, including: X-ray crystallography (HKL-3000, DIALS), NMR (nightshift, protein ligand interaction software (PLIS)), CD (DichroWeb), Cryo-EM (Python-based Helix Indexer (PyHI)), SAXS (SAXSMoW, EFAMIX), MD (SMOG 2/OpenSMOG), protein design (Match_Motif), phylogenetic analysis (PANTHER), and others. Together, these programs are used by tens of thousands of protein scientists per year.

This issue of Protein Science also contains several articles about the Protein Data Bank, including those celebrating the 50th anniversary of the RCSB PDB and the 20th anniversary of PDB Japan (PDBj). Additional PDB-focused articles include one on new features and updates of PDB-101, as well as SARS-CoV-2 and AlphaFold extras on PDBsum.

Exciting new tools described in this special issue are not limited to, but include:

The first-ever genes and protein database of a synthetic organism, the 452-protein-coding gene-containing Mycoplasma mycoides JCVI-syn3A, called SynWiki. This database curates published knowledge about M. mycoides genes and proteins, providing an important resource for synthetic biologists. (Pedreira T, et. al., pp 54-62)

A new program called nightshift that plots chemical shift data from the Biological Magnetic Resonance Data Bank (BMRB) as simulated two-dimensional (2D) and 3D NMR spectra. This tool can be used by NMR experts, as well as structural biologists and protein biochemists with limited NMR knowledge, to utilize the vast amount of publicly-available data in the BMRB. (Fucci IJ and Byrd A, pp 63-74)

A compendium of the 72 monogenic diseases that affect >1:20,000 humans. This includes cystic fibrosis, sickle cell anemia, and several metabolic disorders, amongst many others. This compendium provides an important resource to increase awareness of these monogenic diseases and aid in therapeutic drug targeting, as well as other revolutionary techniques. (Apgar T and Sanders CR, pp75-91)

Growing research indicates that codon usage regulates several aspects of gene and protein expression beyond what is historically appreciated, including, the “net effect of transcription (mRNA synthesis), mRNA half-life, translation (protein synthesis) and the probability of a protein folding correctly to its active, functional structure.” The program CHARMING (for Codon HARMonizING) is presented as a tool to help design mRNA sequences for “heterologous gene expression and other related codon harmonization tasks.” (Wright G, et. al., pp 221-231)

Protein Science 35th Anniversary Symposium Issue 

 Other Special Issues

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July 2021

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March 2020

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March 2020