scholarly journals RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Oncogene ◽  
2020 ◽  
Vol 39 (43) ◽  
pp. 6623-6632
Author(s):  
David S. Goodsell ◽  
Stephen K. Burley
Keyword(s):  
Human Papillomavirus ◽  
Protein Data Bank ◽  
3D Structure ◽  
Healthcare Providers ◽  
Data Bank ◽  
Data Repository ◽  
Biological Macromolecules ◽  
Biologic Drugs ◽  
Related Proteins

Abstract Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.

scholarly journals Citing a Data Repository: A Case Study of the Protein Data Bank

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0136631 ◽  
Author(s):  
Yi-Hung Huang ◽  
Peter W. Rose ◽  
Chun-Nan Hsu
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Data Repository

scholarly journals Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules

1998 ◽  
Vol 54 (6) ◽  
pp. 1078-1084 ◽  
Author(s):  
Joel L. Sussman ◽  
Dawei Lin ◽  
Jiansheng Jiang ◽  
Nancy O. Manning ◽  
Jaime Prilusky ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Protein Data Bank ◽  
Structural Information ◽  
National Laboratory ◽  
Three Dimensional ◽  
Data Bank ◽  
Brookhaven National Laboratory ◽  
Biological Macromolecules

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submittedviaPDB's WWW-based toolAutoDep, in either mmCIF or PDB format, and are most conveniently examinedviaPDB's WWW-based tool3DB Browser.

scholarly journals Disordered Residues and Patterns in the Protein Data Bank

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1522 ◽  
Author(s):  
Mikhail Yu. Lobanov ◽  
Ilya V. Likhachev ◽  
Oxana V. Galzitskaya
Keyword(s):  
Amino Acids ◽  
Statistical Analysis ◽  
Protein Data Bank ◽  
Protein Structures ◽  
3D Structure ◽  
Data Bank ◽  
Disordered Regions

We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB). To obtain such datasets, we clustered the PDB and obtained the groups of chains with different identities and marked disordered residues. We elaborated a new procedure for finding disordered patterns and created a new version of the library. This library includes three sets of patterns: unique patterns, patterns consisting of two kinds of amino acids, and homo-repeats. Using this database, the user can: (1) find homologues in the entire Protein Data Bank; (2) perform a statistical analysis of disordered residues in protein structures; (3) search for disordered patterns and homo-repeats; (4) search for disordered regions in different chains of the same protein; (5) download clusters of protein chains with different identity from our database and library of disordered patterns; and (6) observe 3D structure interactively using MView. A new library of disordered patterns will help improve the accuracy of predictions for residues that will be structured or unstructured in a given region.

The Protein Data Bank: A Case Study in Management of Community Data

2004 ◽  
Vol 1 (1) ◽  
pp. 49-57 ◽  
Author(s):  
Helen Berman ◽  
Philip Bourne ◽  
John Westbrook
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Community Data

scholarly journals Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology

2021 ◽  
Keyword(s):  
Protein Data Bank ◽  
3D Structure ◽  
Deep Understanding ◽  
Data Bank ◽  
Biological Data ◽  
Digital Data ◽  
Internet Resource ◽  
Wide Range ◽  
Great Support ◽  
Data Updating

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RSCB PDB) provides a wide range of digital data regarding biology and biomedicine. This huge internet resource involves a wide range of important biological data, obtained from experiments around the globe by different scientists. The Worldwide Protein Data Bank (wwPDB) represents a brilliant collection of 3D structure data associated with important and vital biomolecules including nucleic acids (RNAs and DNAs) and proteins. Moreover, this database accumulates knowledge regarding function and evolution of biomacromolecules which supports different disciplines such as biotechnology. 3D structure, functional characteristics and phylogenetic properties of biomacromolecules give a deep understanding of the biomolecules’ characteristics. An important advantage of the wwPDB database is the data updating time, which is done every week. This updating process helps users to have the newest data and information for their projects. The data and information in wwPDB can be a great support to have an accurate imagination and illustrations of the biomacromolecules in biotechnology. As demonstrated by the SARS-CoV-2 pandemic, rapidly reliable and accessible biological data for microbiology, immunology, vaccinology, and drug development are critical to address many healthcare-related challenges that are facing humanity. The aim of this paper is to introduce the readers to wwPDB, and to highlight the importance of this database in biotechnology, with the expectation that the number of scientists interested in the utilization of Protein Data Bank’s resources will increase substantially in the coming years.

scholarly journals RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

2020 ◽  
Vol 49 (D1) ◽  
pp. D437-D451 ◽  
Author(s):  
Stephen K Burley ◽  
Charmi Bhikadiya ◽  
Chunxiao Bi ◽  
Sebastian Bittrich ◽  
Li Chen ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Resonance Spectroscopy ◽  
Biological Macromolecules ◽  
Host Cell Proteins ◽  
Global Pandemic ◽  
3D Electron Microscopy ◽  
Fundamental Biology ◽  
Basic And Applied Research ◽  
Research And Education

Abstract 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 RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. 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 (RCSB.org) 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.

Protein Data Bank (PDB): A Database of 3D Structural Information of Biological Macromolecules

2002 ◽  
Author(s):  
Joel L. Sussman ◽  
Frances C. Bernstein ◽  
Jiansheng Jiang ◽  
Michael Libeson ◽  
Dawei Lin ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Structural Information ◽  
Data Bank ◽  
Biological Macromolecules

scholarly journals The history of the PDB as a public resource for enabling science

2014 ◽  
Vol 70 (a1) ◽  
pp. C934-C934
Author(s):  
Helen Berman
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Scientific Community ◽  
Access Point ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Science Technology ◽  
Public Resource ◽  
History Of ◽  
Online Access

As the crystal structures of biological macromolecules were being determined, a new field of structural biology was born. Inspired by these new structures, the scientific community worked to establish a home to archive and share the data emerging from these experiments. The Protein Data Bank (PDB) was established in 1971 with seven structures. The PDB provides a repository for scientists who generate the data, and an access point for researchers and students to find the information needed to drive additional studies. Today, the PDB contains and supports online access to ~100,000 biomacromolecules that help researchers understand aspects of biology, including medicine, agriculture, and biological energy. The ways in which the interrelationships among science, technology, and community have driven the evolution of the PDB resource for more than forty years will be discussed. The PDB archive is managed by the Worldwide Protein Data Bank (wwpdb.org), whose members are the RCSB PDB, PDBe, PDBj and BMRB.

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