PGD specifications


Unique identifier OMICS_21354
Name PGD
Alternative name Protein Geometry Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Version 1.1
Maintained No


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Publication for Protein Geometry Database

PGD citation


Mass and secondary structure propensity of amino acids explain their mutability and evolutionary replacements

Sci Rep
PMCID: 5552740
PMID: 28798365
DOI: 10.1038/s41598-017-08041-7

[…] amino acid conformation in a specific range of (ϕ, ψ) values.We obtained non-parametric density estimates of PX(ϕ, ψ) for each amino acid X from 1,153,791 residues retrieved from the high-resolution protein geometry database (PGD 1.1). In our approach—frequentist—events have a specific probability whose determination depends on the number of observations. Therefore each distribution PX(ϕ, ψ) is g […]

PGD institution(s)
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA; Open Source Lab, Oregon State University, Corvallis, OR, USA
PGD funding source(s)
Supported by National Institutes of Health (R01-GM083136); National Science Foundation (MCB-9982727).

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