Rapid response to emerging biomedical challenges and threats

Abstract

As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.

virusMED: an atlas of hotspots of viral proteins

“…It is also a commonly used tool in many biotechnology applications (Hess & Jewell, 2020; Table 2). Despite the relatively recent emergence of SARS-CoV-2 and its much smaller genome compared with T4 phage, structural biology studies of SARS-CoV-2 proteins are marching forward at an unprecedented pace (Grabowski et al, 2021) and hotspots from 16 distinct proteins have been characterized (Brzezinski et al, 2021). HIV-1 is another virus that has attracted long-standing interest and exhibits 23 protein clusters as defined by the 30% sequence-identity cutoff (Abram et al, 2010).…”

“…virusMED can serve as a blueprint for an Advanced Information System (AIS; pertaining to viruses, as it aims to provide novel analysis and gather information from more specialized databases and web resources. Collection of this information is essential to prepare for any future biomedical threats and challenges (Grabowski et al, 2021) by providing comprehensive and instantaneous avenues of research. The internal flexibility of virusMED allows the easy addition of features to increase the breadth of available data.…”

“…Hotspot analysis can also aid in the design of vaccine immunogens with optimal antigenicity (Lee et al, 2015). The complete genomic information and macromolecular structural information on virtually all structural and nonstructural components in the SARS-CoV-2 genome is highly informative for facilitating the development of preventative and therapeutic agents (Grabowski et al, 2021). For example, NSP3 or 3c-like proteinase structures may guide the development of drugs for the treatment of SARS, while spike glycoprotein-based immunogens are designed to stimulate specific immune responses against SARS-CoV-2 (Hsieh et al, 2020).…”

Some lessons from COVID: science and communication

“…Almost immediately after publication of my 2020 editorial on the rapidity of the structural biology response to the COVID pandemic, I found substantial portions being quoted on Facebook and began receiving emails from family and friends from all around the world. Likewise, Wladek Minor, lead author on an article in the present issue of IUCrJ (Grabowski et al, 2021), tells me that he has never before received such immediate worldwide attention and interest. His article focused on protocols and tools to enable more effective responses to future biomedical threats.…”

Dr. Alexander Wlodawer—celebrating five decades of service to the structural biology community

“…Several collaborative papers were also dedicated to proper validation of atomic models of macromolecules and the identification of 'bad apples' among published results [25][26][27][28][29][30]. Recently, Alex has been instrumental in validating the structures of proteins from the SARS-CoV-2 coronavirus that are rapidly accumulating in the PDB in response to the COVID-19 pandemic [31][32][33][34].…”