Protein Geometry Database

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Protein Geometry Database

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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The Protein Geometry Database (PGD)

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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pgd

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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Other names: The Protein Geometry Database (PGD), pgd

Protein conformation and bond angles and lengths

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Publications

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Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry
PMID: 19906726

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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http://nar.oxfordjournals.org/content/38/suppl_1/D320

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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• Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry PubMed citations: 19.

  19 articles citing: Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry

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  Current Approaches in Supersecondary Structures Investigation. PMID:34769310

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  A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins. PMID:33559613

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  Arginine off-kilter: guanidinium is not as planar as restraints denote. PMID:33263321

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  Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866

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  Dissection of Factors Affecting the Variability of the Peptide Bond Geometry and Planarity. PMID:29164147

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  Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements. PMID:28798365

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  Ensemblator v3: Robust atom-level comparative analyses and classification of protein structure ensembles. PMID:28762605

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  Insights into Thiol-Aromatic Interactions: A Stereoelectronic Basis for S-H/π Interactions. PMID:28080040

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  Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors. PMID:27342939

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  Native proteins trap high-energy transit conformations. PMID:26601321

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  Residue-level global and local ensemble-ensemble comparisons of protein domains. PMID:26032515

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  Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. PMID:24890778

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  Interplay between peptide bond geometrical parameters in nonglobular structural contexts. PMID:24455689

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  Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. PMID:22198840

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  (φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level. PMID:22198294

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  Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures. PMID:21949726

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  A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. PMID:21436958

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  The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. PMID:21034443

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  BriX: a database of protein building blocks for structural analysis, modeling and design. PMID:20972210
• http://nar.oxfordjournals.org/content/38/suppl_1/D320

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structure databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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protein structure

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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protein structural motifs and surfaces

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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proteins

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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protein structure analysis

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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structure prediction

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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protein folds and structural domains

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.924279

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structure protein structure protein structural motifs and surfaces proteins protein structure analysis structure prediction protein folds and structural domains