GRAMM-X statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

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 citations

 (66)
library_books

Binding determinants in the interplay between porcine aminopeptidase N and enterotoxigenic Escherichia coli F4 fimbriae

2018
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) (Additional […]

library_books

Positive Charges on the Surface of Thaumatin Are Crucial for the Multi Point Interaction with the Sweet Receptor

2018
Front Mol Biosci
PMCID: 5816810
PMID: 29487853
DOI: 10.3389/fmolb.2018.00010

[…] (PDB 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 residue […]

library_books

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

2017
Int J Mol Sci
PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] ed 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 prote […]

library_books

Molecular docking based screening of a simulated HIF 1 protein model for potential inhibitors

2017
Bioinformation
PMCID: 5712784
PMID: 29225432
DOI: 10.6026/97320630013388

[…] 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 se […]

library_books

Analysis of the Roles of the Arabidopsis nMAT2 and PMH2 Proteins Provided with New Insights into the Regulation of Group II Intron Splicing in Land Plant Mitochondria

2017
Int J Mol Sci
PMCID: 5713396
PMID: 29149092
DOI: 10.3390/ijms18112428

[…] ces 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 intera […]

call_split

Modulation of the Vault Protein Protein Interaction for Tuning of Molecular Release

2017
Sci Rep
PMCID: 5665922
PMID: 29093465
DOI: 10.1038/s41598-017-12870-x
call_split See protocol

[…] The INT protein based on its amino acid sequence was modeled on I-TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER/). The interaction between MVP and INT was predicted by GRAMM-X protein docking web server (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx). For the prediction, INT was selected as ligand for docking with CP-MVP as the receptor. […]

Citations

Looking to check out a full list of citations?

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

GRAMM-X reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GRAMM-X