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GRAMM-X specifications

Information


Unique identifier OMICS_03773
Name GRAMM-X
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GRAMM-X

GRAMM-X in publications

 (53)
PMCID: 5828407
PMID: 29482635
DOI: 10.1186/s13567-018-0519-9

[…] adopted modeller version 9.17 as the homology modeling tool to develop 3d structures of apn-faeg complexes []. the potential interacted residues in apn-faeg interplay were performed with the help of gramm-x protein–protein docking web server v.1.2.0 [] based on template structures obtained from the protein data bank (pdb id: apn-4fke [], f4ab faeg-4we2, f4ac faeg-2j6r, f4ad faeg-4weu) […]

PMCID: 5816810
PMID: 29487853
DOI: 10.3389/fmolb.2018.00010

[…] entry 3al7, masuda et al., ) with the t1r2-t1r3 sweet receptor were built using the gramm software in a low resolution mode (vasker et al., ). the thaumatin-receptor complexes were refined using gramm-x (http://vakser.bioinformatics.ku.edu). in gramm-x, it is possible to add receptor residues hypothesized to be at the interface of the complex from the low resolution mode and thaumatin […]

PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] conformations using electrostatic interactions or both electrostatic and solvation terms, but the potential is restricted to a correlation function form. fft approaches are very common and include gramm-x which extends the original gramm fft method by employing smoothed potentials, refinement stage, and knowledge-based scoring []. the hex protein docking server (hexserver) is an fft based […]

PMCID: 5712784
PMID: 29225432
DOI: 10.6026/97320630013388

[…] for modeling hif-1 1 and hif-1 2 respectively., we initially opted to model hif-1 1 and hif-12 individually using these two templates. however rigid protein-protein docking programs such as the gramm-x server [] and hex 6.1 were using to 11 and 12 docking studies .the accuracy of homology modelling depends largely on the quality of the alignment between them and template sequence. the low […]

PMCID: 5713396
PMID: 29149092
DOI: 10.3390/ijms18112428

[…] that may serve as rna-binding modules, while the uncharged or negatively charged regions may be required for protein–protein interactions (). nmat2 and pmh2 docking calculations were performed by gramm-x [], with no predetermined bias towards any specific residue interactions, and the predicted structures were visualized by pymol []. the in silico analyses showed that pmh2 and nmat2 may […]


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GRAMM-X institution(s)
Center for Bioinformatics, The University of Kansas, Lawrence, KS, USA

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