Using the Tools and Resources of the RCSB Protein Data Bank

No abstract is available for this paper.

• Publication year

  2005

• Venue

  Current Protocols in Bioinformatics

• Publication date

  2005-03-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1002/0471250953.bi0109s20PMID 18428680
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Searches

  2008cited by this paper
• Structure quality and target parameters

  2006cited by this paper
• Outcome of a workshop on archiving structural models of biological macromolecules.

  2006cited by this paper
• Macromolecular dictionary (mmCIF)

  2006cited by this paper
• PDBML: the representation of archival macromolecular structure data in XML

  2005cited by this paper
• Definition and exchange of crystallographic data

  2005cited by this paper
• Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank.

  2004cited by this paper
• Ligand Depot: a data warehouse for ligands bound to macromolecules

  2004cited by this paper
• The distribution and query systems of the RCSB Protein Data Bank

  2004cited by this paper
• The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

  2004cited by this paper
• Structure validation by Cα geometry: ϕ,ψ and Cβ deviation

  2003cited by this paper
• Announcing the worldwide Protein Data Bank

  2003cited by this paper
• Validation of protein structures for protein data bank.

  2003cited by this paper
• The Protein Data Bank: unifying the archive

  2002cited by this paper
• SCOP database in 2002: refinements accommodate structural genomics

  2002cited by this paper
• Current Protocols in Bioinformatics

  2002cited by this paper
• A standard reference frame for the description of nucleic acid base-pair geometry.

  2001cited by this paper
• Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.

  2001cited by this paper
• The Macromolecular Crystallographic Information File (mmCIF)

  2001cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

  1999cited by this paper
• Protein Data Bank Contents Guide: Atomic Coordinate Entry Format

  1999cited by this paper
• Recommendations for the presentation of NMR structures of proteins and nucleic acids – IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy

  1998cited by this paper
• Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy.

  1998cited by this paper
• Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.

  1998cited by this paper
• A prototype molecular interactive collaborative environment (MICE).

  1998cited by this paper
• SCOP: a structural classification of proteins database

  1998cited by this paper
• Macromolecular Crystallographic Information File.

  1997cited by this paper
• Biological Macromolecule Crystallization Database.

  1997cited by this paper
• [30] Macromolecular crystallographic information file

  1997cited by this paper
• Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution.

  1997cited by this paper
• CATH--a hierarchic classification of protein domain structures.

  1997cited by this paper
• SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling

  1997cited by this paper
• Geometric parameters in nucleic acids: Nitrogenous bases

  1996cited by this paper
• Phi/psi-chology: Ramachandran revisited.

  1996cited by this paper
• Surprising similarities in structure comparison.

  1996cited by this paper
• Errors in protein structures

  1996cited by this paper
• Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents

  1996cited by this paper
• RASMOL: biomolecular graphics for all.

  1995cited by this paper
• PROCHECK: a program to check the stereochemical quality of protein structures

  1993cited by this paper
• A database of protein structure families with common folding motifs

  1992cited by this paper
• The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.

  1992cited by this paper
• Biochemical nomenclature and related documents : a compendium

  1992cited by this paper
• Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement

  1991cited by this paper
• Return

  1988cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper
• \the Protein Data Bank: a Computer-based Archival Le for Macromolecular Structures,"

  year unknowncited by this paper

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