Berlin ab-initio amino acid DB

Description

This database provides structural data of 20 proteinogenic amino acid and their amino-methylated and acetulated (capped) dipeptides and their complex with divalent cations: Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+.

Detailed describtion of database and how it was created can be found from article
"First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids" by Matti Ropo, Markus Schneider, Carsten Baldauf, and Volker Blum.
Scientific Data 3, 160009 (2016) (open access), preprint.

The database is updated (May 2017) to new version of the dataset. Currently NOMAD contain the old version of the dataset.

Alternative method to accedd data is a NoMaD repository

Download database:

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zip-file (74 Mb)

Available system

Schematic figures of amino acids in non-zwitterionic and zwitterionic form, dipeptides and investigated ions
Glycine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Alanine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Leucine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Isoleucine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
GlutamicAcid
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
GlutamicAcidH
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
AsparticAcid
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
AsparticAcidH
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Arginine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
ArginineH
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Lysine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
LysineH
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Glutamine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Asparagine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Cysteine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Methionine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
HistidineD
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
HistidineE
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
HistidineH
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Phenylalanine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Tryptophan
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Proline
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Serine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Threonine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Tyrosine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Valine
Uncapped: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+
Dipeptide: bare Ca2+ Ba2+ Sr2+ Cd2+ Hg2+ Pb2+