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Nucleic Acids Res ; 49(D1): D437-D451, 2021 01 08.
Article in English | MEDLINE | ID: covidwho-936421


The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of users around the world, including >660 000 educators, students and members of the curious public using PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal ( has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

Computational Biology/methods , Databases, Protein , Macromolecular Substances/chemistry , Protein Conformation , Proteins/chemistry , Bioengineering/methods , Biomedical Research/methods , Biotechnology/methods , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Humans , Macromolecular Substances/metabolism , Pandemics , Proteins/genetics , Proteins/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , SARS-CoV-2/physiology , Software , Viral Proteins/chemistry , Viral Proteins/genetics , Viral Proteins/metabolism
Theranostics ; 10(16): 7034-7052, 2020.
Article in English | MEDLINE | ID: covidwho-638462


This review provides an update for the international research community on the cell modeling tools that could accelerate the understanding of SARS-CoV-2 infection mechanisms and could thus speed up the development of vaccines and therapeutic agents against COVID-19. Many bioengineering groups are actively developing frontier tools that are capable of providing realistic three-dimensional (3D) models for biological research, including cell culture scaffolds, microfluidic chambers for the culture of tissue equivalents and organoids, and implantable windows for intravital imaging. Here, we review the most innovative study models based on these bioengineering tools in the context of virology and vaccinology. To make it easier for scientists working on SARS-CoV-2 to identify and apply specific tools, we discuss how they could accelerate the discovery and preclinical development of antiviral drugs and vaccines, compared to conventional models.

Antiviral Agents/isolation & purification , Antiviral Agents/pharmacology , Betacoronavirus , Coronavirus Infections/drug therapy , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/drug therapy , Pneumonia, Viral/prevention & control , Viral Vaccines/isolation & purification , Viral Vaccines/pharmacology , Betacoronavirus/chemistry , Betacoronavirus/genetics , Betacoronavirus/immunology , Bioengineering/methods , Bioengineering/trends , Bioreactors , COVID-19 , COVID-19 Vaccines , Cell Culture Techniques , Computer Simulation , Coronavirus Infections/immunology , Drug Discovery/methods , Drug Discovery/trends , Drug Evaluation/methods , Drug Evaluation/trends , Drug Resistance, Viral , Host Microbial Interactions/genetics , Host Microbial Interactions/immunology , Humans , Models, Biological , Organoids/cytology , Organoids/virology , Pneumonia, Viral/immunology , SARS-CoV-2 , Theranostic Nanomedicine