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DynaMine specifications

Information


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

Maintainer


  • person_outline Elisa Cilia

Publications for DynaMine

DynaMine citations

 (11)
library_books

Exploring the Sequence based Prediction of Folding Initiation Sites in Proteins

2017
Sci Rep
PMCID: 5562875
PMID: 28821744
DOI: 10.1038/s41598-017-08366-3

[…] We used 5 kinds of macro-features computed from the protein sequence using various tools. First, we used DynaMine, to predict the backbone dynamics of each protein. After the prediction, we shifted the dynamics values within each sequence constraining their range between 0 and 1, analogously to Pancsa e […]

call_split

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

2017
Sci Rep
PMCID: 5539115
PMID: 28765603
DOI: 10.1038/s41598-017-07156-1
call_split See protocol

[…] namics in IDPs and that our method significantly surpasses any other method producing comparable information. We also develop a machine learning-based consensus predictor, which uses FRAGFOLD-IDP and DynaMine order parameter predictions to improve protein backbone dynamics predictions even further. […]

library_books

Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP

2017
Sci Rep
PMCID: 5498717
PMID: 28680062
DOI: 10.1038/s41598-017-04611-x

[…] (MoRF). C-terminal regions of β propensity are highly conserved and have a conspicuous enrichment of post-translational modification (PTMs) sites, suggesting functional regulation of this region. The DynaMine profile also shows peaks in this region (Supplementary Fig. , underlined), which together predispose this region for mediating interaction(s) probably not based on induced folding. […]

call_split

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

2017
Sci Rep
PMCID: 5213423
PMID: 28054562
DOI: 10.1038/srep39732
call_split See protocol

[…] ethods, 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 in a st […]

library_books

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

2016
PMCID: 5613702
PMID: 28955936
DOI: 10.1016/j.bbrep.2016.07.018

[…] eins. And also, these high flexibility levels allow to specifically low affinity interactions , , . Rex Protein flexibility analysis was performed by Expasy server using an average flexibility scale, DynaMine server (data not be shown) and Composition Profiler server was performed. They showed high flexibility areas that interrupted by short regions with less flexibility levels (). Based on Rex fl […]

call_split

Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome*

2016
PMCID: 4938175
PMID: 27226608
DOI: 10.1074/jbc.M116.727578
call_split See protocol

[…] The physicochemical properties of 115 sequences were calculated using the following tools: helix propensity, Agadir (); backbone dynamics, DynaMine (, ); disorder propensity, IUPred (); fraction of aliphatic, acidic, basic, nonpolar, aromatic or polar residues: EMBOSS pepstats (); entropy, SEG (, ); flexibility, FLEXPLOT (); and hydropho […]

Citations

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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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