FG-MD protocols

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FG-MD statistics

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FG-MD specifications

Information


Unique identifier OMICS_10837
Name FG-MD
Interface Web user interface
Restrictions to use None
Input data Protein or protein complex structure (C-alpha or full-atomic)
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang <>

Publication for FG-MD

FG-MD in pipelines

 (4)
2017
PMCID: 5519609
PMID: 28729648
DOI: 10.1038/s41598-017-05173-8

[…] the one with the highest value of c-score was selected to be refined closer to the native structure by a molecular dynamics (md) tool called fragment-guided md simulation (fg-md). potential energy of refined protein was estimated by “calculate energy” protocol of discovery studio (ds) 3.0. c3b (template) (pdb id: 2wii) structure was obtained from protein data bank […]

2015
PMCID: 4481407
PMID: 26110638
DOI: 10.1371/journal.pgen.1005260

[…] with the best confidence score (c-score = 0.5) returned by i-tasser was selected. we added hydrogen atoms in this model using haad software [] and refined it close to the native structure using fg-md molecular dynamics based algorithm []., our final refined model of peo was evaluated as a potentially extremely good model (with a predicted lgscore of 2.50) by the pro-q model quality […]

2015
PMCID: 4481533
PMID: 26110528
DOI: 10.1371/journal.pgen.1005167

[…] of ~ 70 aa that have a tendency to be intrinsically disordered. aktip modeling was performed using the composite approach implemented in i-tasser server [] and refined using the haad software fg-md algorithm [, ]. the aktip model was evaluated a potentially extremely good model (with a predicted lgscore of 5.9) by the pro-q model quality assessment program [], and its qmean score [] […]

2013
PMCID: 3682917
PMID: 23497158
DOI: 10.1186/1471-2164-14-174

[…] for this study the top scoring ligand binding site predictions all included heme bound to the conserved iron binding cysteine. for further model refinement the top scoring model was submitted to the fg-md server for fragment guided molecular dynamics structure refinement []. the coordinates for heme were manually transferred to the refined model pdb file and a covalent bond was created […]


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FG-MD in publications

 (29)
PMCID: 5691160
PMID: 29147015
DOI: 10.1038/s41598-017-15837-0

[…] structure elements from the d0 domain of flge onto regions with matching secondary structure predictions (via the i-tasser server) for d0. after refining the hybrid model using iterative steps of fg-md and manual refinement to minimize clashes, we then threaded the complete flgk sequence onto that model using i-tasser to generate a complete monomer structure., an initial structure […]

PMCID: 5678119
PMID: 29118372
DOI: 10.1038/s41598-017-14886-9

[…] the criteria of vadar version 1.8. the huscfv sequences were submitted to i-tasser service for modeling and the models were subsequently refined by modrefiner and fragment guided molecular dynamics (fg-md) simulation for making them become closer to their native state–. the modeled ns5a and the huscfvs were subjected to cluspro2.0 server for determining their contact interface. […]

PMCID: 5591372
PMID: 28928723
DOI: 10.3389/fmicb.2017.01685

[…] models of pre domains were constructed using comparative protein modeling method by i-tasser (). all the structural models were refined in the atomic-level by the fragment-guided molecular dynamics (fg-md) simulations (). the quality assessment of ramachandran plot has been used to quantitatively assess the accuracy of protein structure predictions. the statistical data of ramachandran plot […]

PMCID: 5561080
PMID: 28819150
DOI: 10.1038/s41598-017-08829-7

[…] binding pocket not represented by the kb-752 crystal structure template. the extended giv sequence was re-docked as above and the model was further refined with a fragment-guided molecular dynamics (fg-md) simulation. foldx version 3.0 was used to identify and repair high-energy side-chain conformations. icmpocketfinder was used to predict small molecule-accessible druggable sites on the patch […]

PMCID: 5519609
PMID: 28729648
DOI: 10.1038/s41598-017-05173-8

[…] the one with the highest value of c-score was selected to be refined closer to the native structure by a molecular dynamics (md) tool called fragment-guided md simulation (fg-md). potential energy of refined protein was estimated by “calculate energy” protocol of discovery studio (ds) 3.0. c3b (template) (pdb id: 2wii) structure was obtained from protein data bank […]


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FG-MD institution(s)
Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Mathematics and Computer Science, Central State University, Wilberforce, OH, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
FG-MD funding source(s)
The project is supported in part NSF Career Award (DBI 1027394), and the National Institute of General Medical Sciences (GM083107, GM084222).

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