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DynaMine specifications


Unique identifier OMICS_19044
Name DynaMine
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Output data Some dynamics profile.
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Elisa Cilia <>

Publications for DynaMine

DynaMine citations


Pathways of cellular internalisation of liposomes delivered siRNA and effects on siRNA engagement with target mRNA and silencing in cancer cells

PMCID: 5830644
PMID: 29491352
DOI: 10.1038/s41598-018-22166-3

[…] molecular beacon technology. probing of cellular internalisation pathways by a panel of pharmacological inhibitors indicated that clathrin-mediated (dynamin-dependent) endocytosis, macropinocytosis (dynamine independent), and cell membrane cholesterol dependent process(es) (clathrin and caveolea-independent) all play a role in the sirna-liposomes internalization. the inhibition of either […]


Exploring the Sequence based Prediction of Folding Initiation Sites in Proteins

PMCID: 5562875
PMID: 28821744
DOI: 10.1038/s41598-017-08366-3

[…] accurate picture of such ‘early folding’ residues in proteins, we recently created the start2fold database, which collects data from pulsed labelling and related hdx experiments. we showed that the dynamine sequence-based protein backbone rigidity predictions, give the best results in discriminating early folding residues from other regions of the protein. in addition, we observed that protein […]


Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment Based Protein Structure Predictions

PMCID: 5539115
PMID: 28765603
DOI: 10.1038/s41598-017-07156-1

[…] predict the correct fold of the protein to reliably predict per-residue fluctuations. it implies that disorder is a local property and it does not depend on the fold. our results are orthogonal to dynamine, the only other method significantly better than the naïve prediction. we therefore combine these two using a neural network. fragfold-idp enables better insight into backbone dynamics […]


Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

PMCID: 5213423
PMID: 28054562
DOI: 10.1038/srep39732

[…] all based solely on the knowledge of the protein sequence (). order probability values span from 0, representing a highly dynamic protein residue, to 1, indicating a complete local stability. dynamine was used to predict the s2 order parameter (, black line) for backbone n-h groups, which gives an estimate of likelihood of the protein chain flexibility. although no residue is found […]


Is unphosphorylated Rex, as multifunctional protein of HTLV 1, a fully intrinsically disordered protein? An in silico study

PMCID: 5613702
PMID: 28955936
DOI: 10.1016/j.bbrep.2016.07.018

[…] and doolitle scales were used to determine amino acid hydrophobicity [330]. the average flexibility of rex was calculated by kyte and doolitle scales at (http://web.expasy.org/protscale/) and also dynamine server at (http://dynamine.ibsquare.be/) . charge-hydropathy plot and cdf (cumulative distribution function) analysis (both available at http://www.pondr.com/cgi-bin/pondr/pondr.cgi). use […]


Ubiquitin dependent and independent roles of SUMO in proteostasis

PMCID: 5129774
PMID: 27335169
DOI: 10.1152/ajpcell.00091.2016

[…] parkin as well as sumoylation seem to be involved in mitochondrial fusion and fission, processes with particular importance in brain cells and neurodegeneration. here, it was shown that the dynamine-related protein 1 (drp1) is a target for conjugation by sumo1, sumo2, and sumo3 (). the modification of drp1 by sumo1 led to an increased mitochondrial fission, and senp5 was shown […]

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DynaMine institution(s)
MLG, Computer Science Department, Universite Libre de Bruxelles (ULB), Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium; Department of Structural Biology, VIB, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary; AI-Lab, Computer Science Department, Vrije Universiteit Brussel, Brussels, Belgium
DynaMine funding source(s)
Supported by Brussels Institute for Research and Innovation (Innoviris) [BB2B 2010-1-12]; Belgian Fonds de la Recherche Scientifique (F.R.S.-FNRS) [2.4606.11 and 1.B.05914F]; Research Foundation - Flanders (FWO) [Odysseus G.0029.12].

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