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DIMA specifications


Unique identifier OMICS_02881
Alternative name Domain Interaction MAp
Restrictions to use None
Maintained Yes

Publication for Domain Interaction MAp

DIMA citations


Novel arsenic transforming bacteria and the diversity of their arsenic related genes and enzymes arising from arsenic polluted freshwater sediment

Sci Rep
PMCID: 5593903
PMID: 28894204
DOI: 10.1038/s41598-017-11548-8

[…] them increased the frequency of the other by more than 80%, with a p-value smaller than 10−10. Furthermore, the two residues must have been present in at least 20% of the sequences, as determined by Dima & Thirumalai. For ArsCs, the sequence numbering refers to E. coli ArsC (UniProt code P08692), unless noted. For molybdopterin, A0A0U0D0V4 from Streptococcus pneumoniae was used as the reference.T […]


A Manual Segmentation Tool for Three Dimensional Neuron Datasets

Front Neuroinform
PMCID: 5450622
PMID: 28620293
DOI: 10.3389/fninf.2017.00036

[…] nge (Ascoli, )]. In fact, different tools for the extraction of 3D neural structures have been presented in the literature (Kass et al., ; Osher and Sethian, ; Glaser and Glaser, ; Paragios et al., ; Dima et al., ; Vese and Chan, ; Rohlfing et al., ; Wolf et al., ; Basu et al., ; Mukherjee et al., ; Quan et al., ), but none of them represents a robust system with general applicability. Beyond the […]


2015 Brainhack Proceedings

PMCID: 5103253
DOI: 10.1186/s13742-016-0147-0

[…] PM, Andreassen OA, Arias-Vasquez A, Bearden CE, Boedhoe PS, Brouwer RM, Buckner RL, Buitelaar JK, Bulayeva KB, Cannon DM, Cohen RA, Conrod PJ, Dale AM, Deary IJ, Dennis EL, de Reus MA, Desrivieres S, Dima D, Donohoe G, Fisher SE, Fouche JP, Francks C, Frangou S, Franke B, Ganjgahi H, Garavan H, Glahn DC, Grabe HJ, Guadalupe T, Gutman BA, Hashimoto R, Hibar DP, Holl, D, Hoogman M, Pol HE, Hosten N, […]


Structure Prediction of RNA Loops with a Probabilistic Approach

PLoS Comput Biol
PMCID: 4975501
PMID: 27494763
DOI: 10.1371/journal.pcbi.1005032

[…] effort of structure prediction, merits specific attention. First, this is because RNA functions often reside in loop regions and about 46% of nucleotides in an RNA chain remain unpaired, according to Dima and her colleagues’ research []. Some people mistake loop regions as unstructured. Some people mistake loop regions as structured. There are stacking interactions between neighboring bases, and o […]


Extending Ripley’s K Function to Quantify Aggregation in 2 D Grayscale Images

PLoS One
PMCID: 4670231
PMID: 26636680
DOI: 10.1371/journal.pone.0144404

[…] file was obtained by repeatedly opening the image using progressively larger radii and obtaining the pixel value sum of the resulting image [,].We employed the bivariate similarity index described by Dima et al to illustrate the comparative accuracy and specificity of the two approaches described []. The bivariate similarity index, which is itself an extension of the widely used Jaccard Similary I […]


Comparing human–Salmonella with plant–Salmonella protein–protein interaction predictions

Front Microbiol
PMCID: 4309195
PMID: 25674082
DOI: 10.3389/fmicb.2015.00045

[…] ions (; ; ). Thus, interolog approaches make use of available information from sequence, domain, and PPI databases. Whereas used iPfam and DIP databases as information input to their approach, used DIMA 3.0 and SIMAP databases and obtained domain information from iPfam and 3DID databases, protein sequence information from uniprot and known PPIs from BIANA that integrates available data from 10 […]

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DIMA institution(s)
Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany

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