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
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David S. Goodsell | Zukang Feng | John D. Westbrook | Stephen K. Burley | Chenghua Shao | Andrej Sali | Shuchismita Dutta | Charmi Bhikadiya | Chunxiao Bi | Cole H. Christie | Jose M. Duarte | Rachel Kramer Green | Vladimir Guranovic | Brian P. Hudson | Harry Namkoong | Alexander S. Rose | Monica Sekharan | Yi-Ping Tao | Jasmine Young | Christine Zardecki | Sebastian Bittrich | Joan Segura | Li Chen | Irina Persikova | Yuhe Liang | Catherine L. Lawson | Dmytro Guzenko | Sutapa Ghosh | Sai J. Ganesan | Yana Rose | Gregg V. Crichlow | Kenneth Dalenberg | Luigi Di Costanzo | Sai Ganesan | Robert Lowe | Ezra Peisach | Christopher Randle | Maria Voigt | Marina Zhuravleva | A. Sali | D. Goodsell | J. Westbrook | S. Burley | Robert Lowe | Zukang Feng | Jasmine Y. Young | C. Lawson | Li Chen | E. Peisach | J. Segura | D. Guzenko | C. Zardecki | L. Costanzo | S. Bittrich | Sutapa Ghosh | B. Hudson | C. Shao | G. Crichlow | S. Dutta | Maria Voigt | Irina Persikova | Yuhe Liang | Yi-Ping Tao | Kenneth Dalenberg | Yana Rose | Monica Sekharan | Charmi Bhikadiya | Chunxiao Bi | Vladimir Guranovic | Chris Randle | Harry Namkoong | M. Zhuravleva | Shuchismita Dutta
[1] Wen J. Li,et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..
[2] E. Liu,et al. Company Says It Mapped Part of SARS Virus , 2003 .
[3] David S. Goodsell,et al. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy , 2018, Nucleic Acids Res..
[4] M. Selmer,et al. Structure of the 70S Ribosome Complexed with mRNA and tRNA , 2006, Science.
[5] Haruki Nakamura,et al. Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.
[6] Qiang Zhou,et al. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 , 2020, Science.
[7] Zukang Feng,et al. The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank , 2015, Bioinform..
[8] Z. Rao,et al. Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis , 2019, Nucleic acids research.
[9] Stephen K. Burley,et al. Analysis of impact metrics for the Protein Data Bank , 2018, Scientific Data.
[10] R. Guigó,et al. Cell type–specific genetic regulation of gene expression across human tissues , 2020, Science.
[11] D. Goodsell,et al. Insights from 20 years of the Molecule of the Month , 2020, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.
[12] F. Arnaud,et al. From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory) , 2017 .
[13] Brian McMahon,et al. Definition and exchange of crystallographic data , 2005 .
[14] J. Harrow,et al. A conditional knockout resource for the genome-wide study of mouse gene function , 2011, Nature.
[15] David S. Goodsell,et al. The RCSB Protein Data Bank: new resources for research and education , 2012, Nucleic Acids Res..
[16] Cole H. Christie,et al. Protein Data Bank: the single global archive for 3D macromolecular structure data , 2018, Nucleic Acids Res..
[17] D. Goodsell,et al. Impact of the Protein Data Bank Across Scientific Disciplines , 2020, Data Sci. J..
[18] Sameer Velankar,et al. Mol*: Towards a Common Library and Tools for Web Molecular Graphics , 2018, MolVa@EuroVis.
[19] L. Guddat,et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus , 2020, Science.
[20] Johannes Söding,et al. MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.
[21] Haruki Nakamura,et al. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions , 2008, Journal of biomolecular NMR.
[22] Hualiang Jiang,et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors , 2020, Nature.
[23] The Gene Ontology Consortium,et al. The Gene Ontology Resource: 20 years and still GOing strong , 2018, Nucleic Acids Res..
[24] B. Graham,et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation , 2020, Science.
[25] Stephen K. Burley,et al. Real-time structural motif searching in proteins using an inverted index strategy , 2020, bioRxiv.
[26] Abhik Mukhopadhyay,et al. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe , 2017, Nucleic Acids Res..
[27] A. Godzik,et al. Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2 , 2020 .
[28] David S. Goodsell,et al. The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology , 2015, PLoS biology.
[29] Rajarshi Guha,et al. Pharos: Collating protein information to shed light on the druggable genome , 2016, Nucleic Acids Res..
[30] J. Westbrook,et al. Impact of the Protein Data Bank on antineoplastic approvals. , 2020, Drug discovery today.
[31] J. DiMasi,et al. Landscape of Innovation for Cardiovascular Pharmaceuticals: From Basic Science to New Molecular Entities. , 2017, Clinical therapeutics.
[32] The UniProt Consortium,et al. UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..
[33] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[34] Robert D. Finn,et al. The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..
[35] wwPDB consortium,et al. Protein Data Bank: the single global archive for 3D macromolecular structure data , 2019, Nucleic Acids Res..
[36] S. Miyano,et al. TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES , 2017, bioRxiv.
[37] David S. Goodsell,et al. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education , 2014, Nucleic Acids Res..
[38] Dmytro Guzenko,et al. Real time structural search of the Protein Data Bank , 2020, PLoS computational biology.
[39] A. Walls,et al. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein , 2020, Cell.
[40] A. Joachimiak,et al. The crystal structure of papain-like protease of SARS CoV-2 , 2020 .
[41] Klaus Schulten,et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics , 2013, Nature.
[42] Chenghua Shao,et al. RCSB Protein Data Bank: Enabling biomedical research and drug discovery , 2019, Protein science : a publication of the Protein Society.
[43] David S. Goodsell,et al. The RCSB protein data bank: integrative view of protein, gene and 3D structural information , 2016, Nucleic Acids Res..
[44] Philip E. Bourne,et al. The RCSB PDB information portal for structural genomics , 2005, Nucleic Acids Res..
[45] David S. Goodsell,et al. CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments , 2018, IEEE Computer Graphics and Applications.
[46] D. Goodsell,et al. Integrative illustration for coronavirus outreach , 2020, PLoS biology.
[47] I. Wilson,et al. A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV , 2020, Science.
[48] Benjamin J. Polacco,et al. A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing , 2020, Nature.
[49] James C. Hu,et al. The Gene Ontology Resource: 20 years and still GOing strong , 2019 .
[50] David A. Lee,et al. CATH: an expanded resource to predict protein function through structure and sequence , 2016, Nucleic Acids Res..
[51] Kiyoko F. Aoki-Kinoshita,et al. Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans. , 2017, Carbohydrate research.
[52] Naohiro Kobayashi,et al. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. , 2017, Structure.
[53] David S. Goodsell,et al. The RCSB Protein Data Bank: redesigned web site and web services , 2010, Nucleic Acids Res..
[54] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[55] Amos Bairoch,et al. PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors , 2002, Briefings Bioinform..
[56] S. Perlman,et al. 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice , 2020, Science Translational Medicine.
[57] Philip E. Bourne,et al. The distribution and query systems of the RCSB Protein Data Bank , 2004, Nucleic Acids Res..
[58] Hirofumi Suzuki,et al. New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj) , 2017, Protein science : a publication of the Protein Society.
[59] H. Berg. Cold Spring Harbor Symposia on Quantitative Biology.: Vol. LII. Evolution of Catalytic Functions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1987, ISBN 0-87969-054-2, xix + 955 pp., US $150.00. , 1989 .
[60] David S. Wishart,et al. DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..
[61] T. N. Bhat,et al. The PDB data uniformity project , 2001, Nucleic Acids Res..
[62] Christopher D. Brown,et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues , 2019, Science.
[63] M. Rossmann,et al. Structure of faustovirus, a large dsDNA virus , 2016, Proceedings of the National Academy of Sciences.
[64] Naohiro Kobayashi,et al. Validation of Structures in the Protein Data Bank , 2017, Structure.
[65] Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2 , 2020, Protein science : a publication of the Protein Society.
[66] Zukang Feng,et al. The Protein Data Bank and structural genomics , 2003, Nucleic Acids Res..
[67] Sameer Velankar,et al. BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management , 2020, PLoS Comput. Biol..
[68] J. Westbrook,et al. How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. , 2019, Structure.
[69] Steven E. Brenner,et al. SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures , 2013, Nucleic Acids Res..
[70] T. N. Bhat,et al. The Protein Data Bank: unifying the archive , 2002, Nucleic Acids Res..
[71] Genji Kurisu,et al. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data , 2018, Database J. Biol. Databases Curation.
[72] Christopher D. Brown,et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues , 2019, Science.