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Protocols

MEDELLER specifications

Information


Unique identifier OMICS_17628
Name MEDELLER
Interface Web user interface
Restrictions to use None
Input data The input is a template protein structure and a sequence alignment between the target and template proteins.
Input format PIR, PDB, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Sebastian Kelm

Publication for MEDELLER

MEDELLER citations

 (8)
library_books

Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test case

2017
Sci Rep
PMCID: 5557796
PMID: 28811548
DOI: 10.1038/s41598-017-08344-9

[…] length sequence to a multi sequence alignment). ggTas2r1 has 31% sequence similarity (9% identity) with M2R and 34% sequence similarity (11% identity) with β2AR. Homology modeling was performed with MEDELLER. β2AR and M2R X-ray structures, PDB IDs: 3SN6 and 4MQS, have been used as templates for model 1 and model 2, respectively. ECL2 was modeled using as template the ELC2 of human kappa opioid re […]

library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] methods, it is interesting to note the really outstanding popularity of homology modeling with MODELER . However, for TM protein prediction Kelm et al. presented the TM-specific homology-based tool MEDELLER and used performance analyses to demonstrate that MEDELLER outperforms the most popular homology modeling tool MODELER. The low usability of ab initio techniques is reasonable because they ar […]

call_split

A voltage dependent fluorescent indicator for optogenetic applications, archaerhodopsin 3: Structure and optical properties from in silico modeling

2017
F1000Res
PMCID: 5381632
PMID: 28435665
DOI: 10.5256/f1000research.11514.r19223
call_split See protocol

[…] odopsin-3. Archeorhodopsin-1, which has the highest sequence identity to the target protein, was chosen as a template (RCSB code, 1UAZ). Three algorithms of homology-based model building were tested: Medeller , I-TASSER and RosettaCM . All methods of homology modeling heavily rely on externally made target-template alignment of primary sequences, which serves as the main instruction for model bui […]

call_split

Architecture of the Synaptophysin/Synaptobrevin Complex: Structural Evidence for an Entropic Clustering Function at the Synapse

2015
Sci Rep
PMCID: 4558601
PMID: 26333660
DOI: 10.1038/srep13659
call_split See protocol

[…] The SYP sequence was aligned with the connexin26 sequence based upon a hydropathy window using AlignMe. The aligned sequences were then used in Medeller (http://opig.stats.ox.ac.uk/webapps/medeller/) either as the core SYP 21–220 or the full length sequence as the target and connexin-26 (PDB 2ZW3) as the template. The new model was then dynam […]

library_books

Modeling Suggests TRPC3 Hydrogen Bonding and Not Phosphorylation Contributes to the Ataxia Phenotype of the Moonwalker Mouse

2015
Biochemistry
PMCID: 4530436
PMID: 26112884
DOI: 10.1021/acs.biochem.5b00235

[…] se models. It would also be of possible interest to include the recent TRPA1 channel structure as an additional template, and possibly to compare the output of membrane protein-specific tools such as MEDELLER and/or Rosetta Membrane with those of the used MODELLER. Additionally, a more exhaustive alanine scan of the region of the protein identified in this study and/or the use of non-natural amino […]

call_split

High Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues

2014
PLoS Comput Biol
PMCID: 4031050
PMID: 24854015
DOI: 10.1371/journal.pcbi.1003636
call_split See protocol

[…] The template structures and alignments between template and target sequences for each protein pair in the benchmark were used as inputs to the Homology Modeling software MEDELLER . MEDELLER was run using the online MEDELLER server (http://opig.stats.ox.ac.uk/webapps/medeller/home.pl?app=MEDELLER) with default settings to generate “complete” models. The MEDELLER server […]


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MEDELLER institution(s)
Department of Statistics, University of Oxford, Oxford, UK; UCB Celltech, Branch of UCB Pharma S.A., Slough, UK
MEDELLER funding source(s)
This work was supported by Biotechnology and Biological Sciences Research Council; University of Oxford Doctoral Training Centres.

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