ModRefiner protocols

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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

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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 in pipelines

 (12)
2017
PMCID: 5382200
PMID: 28428776
DOI: 10.3389/fmicb.2017.00592

[…] afpb was predicted by homology modeling using the swiss-model online resource, which selected the protein paf from p. chrysogenum as template for prediction (pdb id 2mhv; ), and refined using the modrefiner tool (figure ). afpb shows 33% amino acid identity and 44% similarity with the p. chrysogenum paf. the refined afpb model showed 56 of 57 (98%) of the amino acid residues positioned […]

2017
PMCID: 5529537
PMID: 28747718
DOI: 10.1038/s41598-017-06575-4

[…] close il-8 sequence from other vertebrates (fig. ). theoretical 3d structural models of human il-8 were constructed using i-tasser server and further refined and energy minimized using modrefiner (table ). the structural consequences of nssnps can be easily ascertained by mapping nssnps onto the corresponding 3d structures of the wild type protein or onto the 3d structures […]

2016
PMCID: 4867070
PMID: 27239476
DOI: 10.1155/2016/8490482

[…] is typically in the range of (−5, 2), where a c-score of higher value signifies a model with a high confidence. the model with the highest c-score was selected and refined by galaxyweb [] and modrefiner [] servers. the models before and after refinement were all validated for their backbone conformation geometry and the residue contact using molprobity []., protein-protein docking […]

2016
PMCID: 4867070
PMID: 27239476
DOI: 10.1155/2016/8490482

[…] similar folds in the protein data bank (pdb) library []. thus, tertiary structures of 14 putative bacteriocin sequences were predicted using i-tasser server [] and then refined by galaxyweb [] and modrefiner [] servers. predicted structures are shown in figure s2 (supplementary material). the percentage of ramachandran favored residues and rotamer favored residues of 14 refined models is 90.2% […]

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

[…] the quality estimation of protein structure models which allow to rank a set of models and to identify potentially unreliable region within protein structure , , ., selected models were redefined by modrefiner server at (http://zhanglab.ccmb.med.umich.edu/modrefiner/). structural conformational search of proteins is conducted by a combination of physic- and knowledge-based force field ., rex […]


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ModRefiner in publications

 (68)
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] 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 […]

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 […]

PMCID: 5867870
PMID: 29518000
DOI: 10.3390/genes9030149

[…] (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 […]

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

[…] 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 […]

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

[…] 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 […]


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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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