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ModRefiner specifications

Information


Unique identifier OMICS_10838
Name ModRefiner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein structure (C-alpha trace, main-chain model or full-atomic model)
Input format PDB
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Yang Zhang

Information


Unique identifier OMICS_10838
Name ModRefiner
Interface Web user interface
Restrictions to use None
Input data Protein structure (C-alpha trace, main-chain model or full-atomic model)
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang

Publication for ModRefiner

ModRefiner citations

 (86)
library_books

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

2018
PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] eviations around the Cα atoms were further refined and optimized from Cα traces, and based on a two-step, atomic-level energy minimization, and to eliminate the residues from disallowed regions using ModRefiner server http://zhanglab.ccmb.med.umich.edu/ModRefiner/ []. Further, the predicted model was evaluated with NMR determined CTD protein structure of AtWRKY4 that comprised of the protein moiet […]

library_books

Molecular characterization of the lipophorin receptor in the crustacean ectoparasite Lepeophtheirus salmonis

2018
PLoS One
PMCID: 5897026
PMID: 29649335
DOI: 10.1371/journal.pone.0195783

[…] of extra-cellular domains (ligand binding domain from repeat R3-R8 and EGF-precursor domain) of LsLpR protein was modelled using Phyre2 online server []. Modelled protein structure was refined using Modrefiner []. Calcium ions binding sites were predicted using Raptor X Binding online server (http://raptorx.uchicago.edu/BindingSite/) or COACH for protein-ligand binding site prediction (http://zha […]

library_books

Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage

2018
Genes
PMCID: 5867870
PMID: 29518000
DOI: 10.3390/genes9030149

[…] s (PDB id: 3TC3) []. Based on these template structures, 200 models were initially generated using Modeller v9.14 [] and ranked using discrete optimized protein energy (DOPE) potential scores []. The ModRefiner program was then used for the refinement of selected models []. The secondary structure elements in the regions containing CSIs were examined and compared with results of the PSIPRED analys […]

library_books

Building protein protein interaction networks for Leishmania species through protein structural information

2018
BMC Bioinformatics
PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] says of protein interaction, it is often necessary to perform a full-atomic refinement simulation to increase the quality of the models [, ]. Therefore, all predicted structures were submitted to the Modrefiner [] refinement algorithm.The quality of the models was evaluated against stereochemical and energetic parameters using Procheck [] tool and against the standard Discrete Optimized Protein En […]

library_books

Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1

2018
Sci Rep
PMCID: 5832771
PMID: 29497085
DOI: 10.1038/s41598-018-21952-3

[…] ons. The generated models were ranked with TopScore, and the highest ranked model for each template combination was selected for model combination and refinement. The selected models are refined with ModRefiner and scored with TopScore. Based on TopScore predictions, regions with errors are removed and the remaining regions used as templates to construct meta-models. Two iterations of this refinem […]

library_books

Leishmania infantum 5’ Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target

2017
BMC Struct Biol
PMCID: 5738077
PMID: 29258562
DOI: 10.1186/s12900-017-0079-7

[…] ated for each submitted protein sequence, ranked according to their C-scores as an estimate of their quality []. The model with the best (highest) C-score was retained and further refined through the ModRefiner server []. Predictions on functional annotations of each protein based on proteins structurally related to the predicted 3D model were provided by I-TASSER. This included Enzyme Commission […]

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ModRefiner institution(s)
Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
ModRefiner funding source(s)
This work was supported by a National Science Foundation Career Award (DBI 1027394) and grants from the National Institute of General Medical Sciences (GM083107 and GM084222).

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