pgd.science.oregonstate.edu

Protein Geometry Database

The PGD allows you to explore either protein conformation or protein covalent geometry or the correlations between protein conformation and bond angles and lengths. Search results appear on an interactive plot which defaults to a Ramachandran plot. Any conformational angle, bond length, or bond angle of any of the residues in the motif can be plotted. The colors can indicate the observational density or the value of any of the other stereochemical properties of any other residue. Berkholz, D.S., ...

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Protein Geometry Database | pgd.science.oregonstate.edu Reviews

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The PGD allows you to explore either protein conformation or protein covalent geometry or the correlations between protein conformation and bond angles and lengths. Search results appear on an interactive plot which defaults to a Ramachandran plot. Any conformational angle, bond length, or bond angle of any of the residues in the motif can be plotted. The colors can indicate the observational density or the value of any of the other stereochemical properties of any other residue. Berkholz, D.S., ...

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Protein Geometry Database | pgd.science.oregonstate.edu Reviews

https://pgd.science.oregonstate.edu

The PGD allows you to explore either protein conformation or protein covalent geometry or the correlations between protein conformation and bond angles and lengths. Search results appear on an interactive plot which defaults to a Ramachandran plot. Any conformational angle, bond length, or bond angle of any of the residues in the motif can be plotted. The colors can indicate the observational density or the value of any of the other stereochemical properties of any other residue. Berkholz, D.S., ...

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Protein Geometry Database

http://pgd.science.oregonstate.edu/references

Berkholz, D.S., Krenesky, P.B., Davidson, J.R., and Karplus, P.A. (2010) Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. Database issue, D320-D325. Selecting the protein chains in the PGD database:. Wang,G. and Dunbrack,R.L. (2003) PISCES: a protein sequence culling server. Classifying residues by secondary structure:. Publications which used the PGD:. So it can be included here. Karplus, P.A., Shapovalov, M.V., ...

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dunbrack.fccc.edu

P20 :: Dunbrack Lab

http://dunbrack.fccc.edu/nmhrcm

Conformation-dependent library for backbone geometry in proteins. Rama(φ,ψ). Peptide ω(φ,ψ). Conformation-dependent library for backbone geometry in proteins. You can download the conformation-dependent backbone geometry library in an uncompressed, text format. Or in a zip archive. The text format is both human- and computer-friendly. The library file has Quick-Start information in its header. The publication of this work ( pdf with supplemental figures included. And its supplemental figures here.

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pgd.science.oregonstate.edu

Protein Geometry Database

The PGD allows you to explore either protein conformation or protein covalent geometry or the correlations between protein conformation and bond angles and lengths. Search results appear on an interactive plot which defaults to a Ramachandran plot. Any conformational angle, bond length, or bond angle of any of the residues in the motif can be plotted. The colors can indicate the observational density or the value of any of the other stereochemical properties of any other residue. Berkholz, D.S., ...

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