gmfit
a program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)
LastModified: 2023/07/22
- July 22,2023: All GMMs for PDBs and surface obj files for EMDB have been updated, independent of EM navigator.
- May 27,2021: The server have been moved to the new WEB server machine with the same address. The function MolMil viewer in PairwiseGmfit has been improved.
- May 4,2018: The licence information (LGPLv3) is announuced for the source codes for gmconvert and
gmfit.
- Mar 6,2018: The paper about Gaussian-input GMM is available online.
- Oct 18,2017:
The WEB server for the gmfit have been moved to "https://pdbj.org/gmfit".
- Feb 26,2016:
The pairwise gmfit page now can accept a user-uploaded map file and a pdb file.
- Feb 26,2015:
The Omokage Search and
EM Navigator pages have links to
gmfit pairwise superposition page.
- Jan 28,2015: The new source code for the program gmconvert is open. It can read mmCIF file with assembly_id, and employs the GMM-input EM algorithm as the default.
- Oct 27,2013: Test page for pairwise GMM fitting "Pairwise GMM Fit" between EMDB and PDB is now available.
- Apr 13,2013:Source codes of gmfit and gmconvert programs are now open.
Please access download page.
Outline
The program gmfit is developed to superimpose several subunit atomic models determined by X-ray crystallograph or NMR
into the low resolution 3D density map detemined by electron microscopy.
This superimposition generally requires large computatinal costs, because the atomic models often contains
103--104 atoms, and 3D density map contains 105--106 grids.
We employed Gaussian Mixture Model (GMM) to approximate shapes of atomic models and 3D density map.
GMM is a distribution function consisting of linear combinations of several Gaussian functions.
The GMM enables us to quickly calculate the fitness of the density map and subunit models,
because the overlap of the product of two Gaussian functions can be analyticaly obtained.
We prepare two programs for fitting.
The program gmconvert converts various models of molecules (atomic model, 3D density map) into GMM.
The program gmfit superimposes GMM subunits into the GMM density map of the complex.
Download the source codes
Source codes of gmfit and gmconvert programs are freely downloadable from the download page.
They are mainly written in C language, supposed to be executed in the Linux environment.
Manuals of the programs
- gmconvert: converting atomic model/density map into GMM.
- gmfit: fitting GMM subunits into GMM complex.
Future plan
The current version of gmfit program can only handle a rigid-body fitting of molecule represented by GMM.
We know including interaction of subunit atomic models, and flexible transformation of subunits are necessary
for more accurate modeling. We are now planning to develop the refinement of GMM models by atomic model,
and flexible transformation of subunit models.
If you have a question and a suggestion about gmfit, please contact to
Takeshi Kawabata.
Example of GMM (Gaussian Mixture Model)
- Example of GMM for atomic model
- Example of GMM for 3D density map
Contact
References
- Kawabata, T.
Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.
Biophys J 2008 Nov 15;95(10):4643-58.
[Publisher]
[PubMed]
- Suzuki H, Kawabata T, Nakamura H.
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Bioinformatics. 2016 Feb 15;32(4):619-20. doi: 10.1093/bioinformatics/btv614. Epub 2015 Oct 27.
[Publisher]
[PubMed]
- Kawabata, T. Gaussian-input Gaussian mixture model for representing density maps and atomic models. J Struct Biol. 2018 Mar 6. pii: S1047-8477(18)30064-9. doi: 10.1016/j.jsb.2018.03.002.
[Publisher]
[PubMed]
Links
[PairwiseGmfit]
