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Literature DB >> 23023942

The future of the Protein Data Bank.

Helen M Berman¹, Gerard J Kleywegt, Haruki Nakamura, John L Markley.

Abstract

The Worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The wwPDB's mission is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Its members [RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and BMRB (USA)] host data-deposition sites and mirror the PDB ftp archive. To support future developments in structural biology, the wwPDB partners are addressing organizational, scientific, and technical challenges.

Entities: Chemical Species

Mesh：

Year: 2012 PMID： 23023942 PMCID： PMC3684242 DOI： 10.1002/bip.22132

Source DB: PubMed Journal: Biopolymers ISSN： 0006-3525 Impact factor: 2.505

23 in total

1. Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR.

Authors: Tomasz L Religa; Remco Sprangers; Lewis E Kay
Journal: Science Date: 2010-04-02 Impact factor: 47.728

2. Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.

Authors: Matthew J Belousoff; Tal Shapira; Anat Bashan; Ella Zimmerman; Haim Rozenberg; Kenji Arakawa; Haruyasu Kinashi; Ada Yonath
Journal: Proc Natl Acad Sci U S A Date: 2011-01-31 Impact factor: 11.205

3. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.

Authors: Vadim Cherezov; Daniel M Rosenbaum; Michael A Hanson; Søren G F Rasmussen; Foon Sun Thian; Tong Sun Kobilka; Hee-Jung Choi; Peter Kuhn; William I Weis; Brian K Kobilka; Raymond C Stevens
Journal: Science Date: 2007-10-25 Impact factor: 47.728

4. The Protein Data Bank: a historical perspective.

Authors: Helen M Berman
Journal: Acta Crystallogr A Date: 2007-12-21 Impact factor: 2.290

5. The structure of the potassium channel: molecular basis of K+ conduction and selectivity.

Authors: D A Doyle; J Morais Cabral; R A Pfuetzner; A Kuo; J M Gulbis; S L Cohen; B T Chait; R MacKinnon
Journal: Science Date: 1998-04-03 Impact factor: 47.728

6. Crystal structure of a TFIIB-TBP-TATA-element ternary complex.

Authors: D B Nikolov; H Chen; E D Halay; A A Usheva; K Hisatake; D K Lee; R G Roeder; S K Burley
Journal: Nature Date: 1995-09-14 Impact factor: 49.962

7. REFMAC5 for the refinement of macromolecular crystal structures.

Authors: Garib N Murshudov; Pavol Skubák; Andrey A Lebedev; Navraj S Pannu; Roberto A Steiner; Robert A Nicholls; Martyn D Winn; Fei Long; Alexei A Vagin
Journal: Acta Crystallogr D Biol Crystallogr Date: 2011-03-18

8. Representation of viruses in the remediated PDB archive.

Authors: Catherine L Lawson; Shuchismita Dutta; John D Westbrook; Kim Henrick; Helen M Berman
Journal: Acta Crystallogr D Biol Crystallogr Date: 2008-07-17

9. BioMagResBank.

Authors: Eldon L Ulrich; Hideo Akutsu; Jurgen F Doreleijers; Yoko Harano; Yannis E Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F Schulte; David E Tolmie; R Kent Wenger; Hongyang Yao; John L Markley
Journal: Nucleic Acids Res Date: 2007-11-04 Impact factor: 16.971

10. Remediation of the protein data bank archive.

Authors: Kim Henrick; Zukang Feng; Wolfgang F Bluhm; Dimitris Dimitropoulos; Jurgen F Doreleijers; Shuchismita Dutta; Judith L Flippen-Anderson; John Ionides; Chisa Kamada; Eugene Krissinel; Catherine L Lawson; John L Markley; Haruki Nakamura; Richard Newman; Yukiko Shimizu; Jawahar Swaminathan; Sameer Velankar; Jeramia Ory; Eldon L Ulrich; Wim Vranken; John Westbrook; Reiko Yamashita; Huanwang Yang; Jasmine Young; Muhammed Yousufuddin; Helen M Berman
Journal: Nucleic Acids Res Date: 2007-12-11 Impact factor: 16.971

28 in total

1. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Authors: Jasmine Y Young; John D Westbrook; Zukang Feng; Raul Sala; Ezra Peisach; Thomas J Oldfield; Sanchayita Sen; Aleksandras Gutmanas; David R Armstrong; John M Berrisford; Li Chen; Minyu Chen; Luigi Di Costanzo; Dimitris Dimitropoulos; Guanghua Gao; Sutapa Ghosh; Swanand Gore; Vladimir Guranovic; Pieter M S Hendrickx; Brian P Hudson; Reiko Igarashi; Yasuyo Ikegawa; Naohiro Kobayashi; Catherine L Lawson; Yuhe Liang; Steve Mading; Lora Mak; M Saqib Mir; Abhik Mukhopadhyay; Ardan Patwardhan; Irina Persikova; Luana Rinaldi; Eduardo Sanz-Garcia; Monica R Sekharan; Chenghua Shao; G Jawahar Swaminathan; Lihua Tan; Eldon L Ulrich; Glen van Ginkel; Reiko Yamashita; Huanwang Yang; Marina A Zhuravleva; Martha Quesada; Gerard J Kleywegt; Helen M Berman; John L Markley; Haruki Nakamura; Sameer Velankar; Stephen K Burley
Journal: Structure Date: 2017-02-09 Impact factor: 5.006

2. A novel approach to represent and compare RNA secondary structures.

Authors: Eugenio Mattei; Gabriele Ausiello; Fabrizio Ferrè; Manuela Helmer-Citterich
Journal: Nucleic Acids Res Date: 2014-04-21 Impact factor: 16.971

3. Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets.

Authors: Eduardo Habib Bechelane Maia; Vinícius Alves Campos; Bianca Dos Reis Santos; Marina Santos Costa; Iann Gabriel Lima; Sandro J Greco; Rosy I M A Ribeiro; Felipe M Munayer; Alisson Marques da Silva; Alex Gutterres Taranto
Journal: J Mol Model Date: 2017-01-07 Impact factor: 1.810

The future of the Protein Data Bank.

1. Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR.

2. Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.

3. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.

4. The Protein Data Bank: a historical perspective.

5. The structure of the potassium channel: molecular basis of K+ conduction and selectivity.

6. Crystal structure of a TFIIB-TBP-TATA-element ternary complex.

7. REFMAC5 for the refinement of macromolecular crystal structures.

8. Representation of viruses in the remediated PDB archive.

9. BioMagResBank.

10. Remediation of the protein data bank archive.

1. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

2. A novel approach to represent and compare RNA secondary structures.

3. Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets.

4. Redundancy-weighting for better inference of protein structural features.

Review 5. Modelling three-dimensional protein structures for applications in drug design.

Review 6. Towards precision medicine: advances in computational approaches for the analysis of human variants.

Review 7. Crystallographic model validation: from diagnosis to healing.

8. Structure of Vibrio cholerae ribosome hibernation promoting factor.

9. An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

10. Dependence of protein crystal stability on residue charge states and ion content of crystal solvent.