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DADP specifications


Unique identifier OMICS_05703
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Davor Juretic

Publication for DADP

DADP citations


Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

PMCID: 4728125
PMID: 26754917
DOI: 10.7554/eLife.07141
call_split See protocol

[…] .0.4 (Schrödinger, LLC). Final refinement statistics are shown in . In addition to the substrate/specificity effector pairs bound in each structure, all structures have dATP or its hydrolysis product dADP in the allosteric activity site. In some cases, the high concentration of nucleotide used (10 mM) has resulted in more than one nucleotide molecule bound near this allosteric site. […]


A Large Scale Structural Classification of Antimicrobial Peptides

Biomed Res Int
PMCID: 4426897
PMID: 26000295
DOI: 10.1155/2015/475062
call_split See protocol

[…] ADAM contains 7,007 unique AMP sequences extracted from twelve databases (). The twelve databases include APD2 [], AVPpred [], BACTIBASE [], BAGEL3 [], CAMP2 [], DADP [], DAMPD [], HIPdb [], PenBase [], PhytAMP [], RAPD [], and YADAMP []. The AMP sequences in ADAM were mostly derived from natural sources, covering a broad spectrum of species such as archaea, b […]


Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure based mechanistic dissection of a molecular motor

PMCID: 3940203
PMID: 24531492
DOI: 10.1107/S1399004713030629
call_split See protocol

[…] l ClpB NBD2 variants were grown in a hanging-drop vapour-diffusion setup at 20°C. The protein solution (∼8 mg ml−1 in buffer A) was either nucleotide-free or was supplemented with 2 mM ADP, 2 mM MANT-dADP or 2 mM AMPPCP and was mixed in a 1:1 ratio with the reservoir solutions. Crystals of wild-type ClpB NBD2 (space group P65) in the nucleotide-free state and in complex with ADP or with AMPPCP gre […]


Exploration of the core metabolism of symbiotic bacteria

BMC Genomics
PMCID: 3543179
PMID: 22938206
DOI: 10.1186/1471-2164-13-438

[…] nother bacterium, and we grouped and compared them among organisms. In this analysis, the following compounds were removed since they are only produced by reactions which also involve macromolecules: dADP, dCDP, dUDP, dGDP. Hence, a systematic search for the inputs in the small molecule metabolism would indicate these compounds as potential inputs, whereas they in fact can be produced by the cell. […]


Diverse substrate recognition and hydrolysis mechanisms of human NUDT5

Nucleic Acids Res
PMCID: 3203587
PMID: 21768126
DOI: 10.1093/nar/gkr575
call_split See protocol

[…] P was determined by using the phase data from the ADPR-binding structure (PDB code: 2DSC). Refinement was carried out with CNS and PHENIX (,).The structures of hNUDT5-8-oxo-dGDP-Mn2+ and hNUDT5-8-oxo-dADP-Mn2+ were determined using the phase data from the hNUDT5-8-oxo-dGMP structure. Refinements of each structure were carried out with CNS and subsequently with REFMAC5 (,), including refinement of […]


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DADP institution(s)
Department of Physics, Faculty of Science, University of Split, Split, Croatia; Centre for Informatics and Computing, Ruder Boškovic Institute, Zagreb, Croatia; Department of Life Sciences, University of Trieste, Trieste, Italy
DADP funding source(s)
Supported by Croatian Ministry of Science, Education and Sport (Grant No. 177-1770495-0476).

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