FG-MD statistics

info info

Citations per year


Popular tool citations

chevron_left Structure refinement chevron_right

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?


FG-MD specifications


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


  • person_outline Yang Zhang

Publication for FG-MD

FG-MD citations


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

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 […]


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

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. […]


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

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 […]


The Gαi GIV binding interface is a druggable protein protein interaction

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 […]


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

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 […]


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

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 […]

Want to access the full list of citations?
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).

FG-MD reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FG-MD