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Protocols

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 citations

 (30)
library_books

Structure of FlgK reveals the divergence of the bacterial Hook Filament Junction of Campylobacter

2017
Sci Rep
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 […]

library_books

Human single chain transbodies that bound to domain I of non structural protein 5A (NS5A) of hepatitis C virus

2017
Sci Rep
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. […]

library_books

Analysis of the Sequences, Structures, and Functions of Product Releasing Enzyme Domains in Fungal Polyketide Synthases

2017
Front Microbiol
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 […]

library_books

The Gαi GIV binding interface is a druggable protein protein interaction

2017
Sci Rep
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 […]

library_books

A haplotype in CFH family genes confers high risk of rare glomerular nephropathies

2017
Sci Rep
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 […]

library_books

3D QSAR and Molecular Docking Studies on the TcPMCA1 Mediated Detoxification of Scopoletin and Coumarin Derivatives

2017
Int J Mol Sci
PMCID: 5535873
PMID: 28653986
DOI: 10.3390/ijms18071380

[…] to refine the structural models, a second round of structure reassembly is conducted starting from the spicker clusters. the low free-energy conformations refined by full-atomic simulations using fg-md [] and modrefiner []. finally, the biological functions of the target proteins were derived by matching the i-tasser models with proteins in the biolip library [,,]., based on identity […]


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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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