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MaxOcc specifications

Information


Unique identifier OMICS_20008
Name MaxOcc
Alternative name Maximum Occurrence
Restrictions to use None
Input data NMR data and SAXS profiles.
Computer skills Basic
Maintained Yes

Maintainers


  • person_outline Claudio Luchinat
  • person_outline Ivano Bertini

Publication for Maximum Occurrence

MaxOcc citations

 (4)
library_books

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

2018
PMCID: 5920944
PMID: 29297679
DOI: 10.1021/acs.chemrev.7b00427

[…] of flexibility suggested for kink-turns, (). Such motions are detectable by analyzing RDCs but not spin relaxation data. The MD trajectory was also compared to NMR data using the maximum occurrence (MaxOcc) method, which analyzes averaged experimental RDCs by weighting contributions of a set of sterically allowed conformations.A series of 1 μs AMBER bsc0 simulations of the isolated TAR using star […]

library_books

Combining NMR and small angle X ray scattering for the study of biomolecular structure and dynamics

2017
PMCID: 5553349
PMID: 28501583
DOI: 10.1016/j.abb.2017.05.005

[…] ion.An interesting extension of the ensemble approach combining SAXS and NMR data from pseudocontact shifts (PCS), Paramagnetic Relaxation Enhancements (PREs) and residual dipolar couplings (RDCs) is Maximum Occurrence analysis (MO) , . In this approach the conformational heterogeneity of two-domain proteins is assessed through the estimation of a MO parameter for each conformation in an ensemble […]

library_books

Synergistic Applications of MD and NMR for the Study of Biological Systems

2012
PMCID: 3272818
PMID: 22319241
DOI: 10.1155/2012/254208

[…] es and MD simulations in order to create relatively small ensembles of conformers for which the populations weights are then optimized using experimental data. The maximum occurrence approach (termed MaxOcc) [, ] also uses weights (in this case defined as the maximum fraction of time a conformer can exist such that experiment data is well reproduced). The originality of this approach lies in the f […]

call_split

A multispecies comparison of the metazoan 3' processing downstream elements and the CstF 64 RNA recognition motif

2006
BMC Genomics
PMCID: 1539018
PMID: 16542450
DOI: 10.1186/1471-2164-7-55
call_split See protocol

[…] example motifs tabulated. The MEME program was run a beowulf cluster using options "-dna -mod oops -nmotifs 3 -text -p52 -maxsize 1000000". Improbizer runs used options "numMotifs = 3 background = l maxOcc = l" and for additional control runs the "controlRun = on" parameter was set. Motif sequence information was gathered from all three programs via perl script and used to make sequence logo [] i […]


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MaxOcc institution(s)
Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Sesto Fiorentino, Italy; EMBL, Hamburg Outstation, Hamburg, Germany
MaxOcc funding source(s)
Supported by MIUR-FIRB contracts RBLA032ZM7, RBRN07BMCT, and by the European Commission, contracts Bio-NMR n. 261863, East-NMR n. 228461, Biomedbridges n. 284209 and We-NMR 261572; and by the national GRID Initiatives of Belgium, Italy, Germany, the Netherlands (via the Dutch BiG Grid project), Portugal, the United Kingdom, South Africa, Taiwan and the Latin America GRID infrastructure via the Gisela project.

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