MMM protocols

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MMM specifications

Information


Unique identifier OMICS_28253
Name MMM
Alternative name Multiple Mapping Method
Interface Web user interface
Restrictions to use None
Input data A target sequence.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Andras Fiser <>

Publications for Multiple Mapping Method

MMM in pipeline

2015
PMCID: 4477651
PMID: 25969444
DOI: 10.1093/nar/gkv410

[…] core domain (ccd). in solution, the isolated mlv in ctd adopts an sh3 domain fold flanked by a c-terminal unstructured tail. we generated a concordant mlv in ccd structural model using swiss-model, mmm-tree and i-tasser. using the x-ray crystal structure of the prototype foamy virus in target capture complex together with our mlv domain structures, residues within the ccd α2 helical region […]


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MMM in publications

 (9)
PMCID: 5448097
PMID: 28373283
DOI: 10.1074/jbc.M116.769505

[…] what-if () and swiss-model structural assessment () web servers. this predicted wild-type model was then used as a template in the homology modeling of the mutated n-terminal β1 peptides using the multiple mapping method (mmm) web server (). mmm combines the best alternatively aligned fragments along the peptide into a final alignment used for the model construction. all the predicted mutant […]

PMCID: 5316886
PMID: 28195158
DOI: 10.1038/ncomms14401

[…] between xiap and bendless. blast searches using bendless (b7pkk7) and xiap (b7pf95) sequences were evaluated against the pdb. predicted structures with the highest homology where modelled using the multiple mapping method and phyre2 programs. the software zdock was used to model the xiap-bendless complex. top ten predictions, which localize to a single interface were shown. visualization […]

PMCID: 4749091
PMID: 26755705
DOI: 10.1084/jem.20150785

[…] inc.). pvrl4 (protein data bank accession no. 4jjh) was selected as the template for comparative protein structure modeling. the structural model of the igv domain of cd112r was constructed with the multiple mapping method server using the optimal combination of two alignment methods, muscle (european bioinformatics institute) and hhalign (max planck institute)., the extracellular domains […]

PMCID: 4477651
PMID: 25969444
DOI: 10.1093/nar/gkv410

[…] and viral replication was assessed by the presence of reverse transcriptase in the culture media ()., an automated approach was taken for obtaining the model of mlv ccd in using the swiss-model (–), mmm-tree () and i-tasser (–) servers. for all servers, the pfv in ccd target capture complex (pdb id:3os1) was selected as template since we were interested in obtaining information for residues […]

PMCID: 4040991
PMID: 24751979
DOI: 10.1093/gbe/evu083

[…] under positive selection. posterior probabilities for each site to belong to the site class with an ω value >1 were extracted from the paml results., the structure of cyp318a1 was modeled using mmm model (). the nearest structural neighbor to the d. melanogaster enzyme as stated in the ncbi protein database is the structure of the human microsomal cyp3a4 (pdb 1tqn) and was used […]


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MMM institution(s)
Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine, Bronx, New York, NY, USA
MMM funding source(s)
Supported by the Howard Hughes Medical Institute, the Seaver Foundation, and NIH with GM62519-04.

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