ModRefiner pipeline

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

 (3)
2017
PMCID: 5382200
PMID: 28428776
DOI: 10.3389/fmicb.2017.00592

[…] by homology modeling using the swiss-model online resource, which selected the protein paf from p. chrysogenum as template for prediction (pdb id 2mhv; fizil et al., 2015), and refined using the modrefiner tool (figure 1). 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 […]

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

[…] folds in the protein data bank (pdb) library [37]. thus, tertiary structures of 14 putative bacteriocin sequences were predicted using i-tasser server [25] and then refined by galaxyweb [26] and modrefiner [27] servers. predicted structures are shown in figure s2 (supplementary material). the percentage of ramachandran favored residues and rotamer favored residues of 14 refined models […]

2014
PMCID: 4330267
PMID: 25705171
DOI: 10.5808/GI.2014.12.4.283

[…] wild type and mutant) were performed using the protein fold recognition server phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/) with 100% confidence. the predicted models were energetically minimized in modrefiner (http://zhanglab.ccmb.umich.edu/modrefiner/) to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology, and side chain positioning. […]

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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